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Isaac's basement is one of many portals to hell
These portals lure in lost souls by slowly driving them mad with the compulsion to slaughter their loved ones and each other. That's why Isaac's mother started hearing commands from "God" to murder her son. The corruption drives people to use painful self-mutilating power-ups to increase their ability to hurt one another. The enemies you fight were once normal human beings (many of which were other children). Hence, Isaac's mother is human in the intro but transforms herself into an Eldritch Abomination by the time you fight her. Children's tears and human blood injure these tainted beings, but that fact only drives them to weaponize their last vestiges of humanity.

Isaac's gestation irrevocably damaged his mother. All subsequent pregnancies resulted in miscarriages.
That's why Mom tried to dress Isaac as the daughter she always wanted, that's why she became so tormented and neglected Isaac like he was a curse, that's why Isaac's father left.

Neglected, Isaac slowly starts to understand that his mother rues his existence. It's why Isaac's imaginary ventures are tormented by visions of himself, killing his half-formed and broken potential siblings and eventually tearing through his mother's internals. It's why Isaac wishes so badly that he could destroy himself in the womb, before he destroyed her. His imaginings are all recorded in the form of his drawings ("I was killed by...").

When he sees his mother finding solace from her grief in her faith, he flips open a Bible. He's terrified. "This kid is called Isaac! I bet Mom wants me dead too!" Gameplay is a psychonautical mental battle, for Isaac's belief in his right to exist. The different playable characters are his different personality facets; Satan is his sins, Isaac 2 is his resulting regret at existing (that's why "II"ssac looks so happy when he dies), and ??? is his subsequent suicidal urges.

When he tries to suffocate himself at the end of the game, he's not trying to escape. He's trying to ease his mother's suffering, to stop her from being constantly reminded that she's barren, and that she subjected so many sentient fetii to horrible deaths. He wants to be forgotten.

The polaroids, memories of a time before the complications, flash before his fading eyes. The ending is a deliberate cliffhanger. Will he conquer his fears and open the box again? It's down to you, tropers.

  • As an astute fellow further down pointed out, "Sister Maggy" later turns up as a floating stillborn fetus. I cite that as supporting evidence.
  • "Psychonautical?"
  • Actually, in the ending of The Chest, Maggy was a real sibling of isaac's. Mom liked her more than Isaac, but something seems to have happened to her.
    • The final ending in Afterbirth+ (and the final ending of Afterbirth before it) confirm that Isaac died in the chest.

Larry Jr. is a successful experiment of a human centipede
This boss has a kind of similar behavior to the Centipede, and he (or rather they) shits everywhere while you fight him, thus the WMG. Well, if he isn't human now, he might have been at some point.
  • Also, try looking carefully at his head. He's crying.
  • Sometimes when you shoot the body, Larry Jr. splits into two. Now, where would the other head come from? From the body. It's not separate segments. These are actual heads connected into a centipede.
  • This is supported by the "buttlicker" enemies, each separate heads connected into a chain, and who are most likely in the process of becoming a Larry Jr.

??? is suicide incarnate.
Isaac clearly has some thoughts of suicide, wanting to destroy his unborn self, shutting himself in the toybox, and all that. Maybe ??? is a possible-future dead Isaac — that's irrelevant. In-game, ??? is incredibly weak, has no capacity to heal, and a tendency to draw flies. He's suicidal for the player.

The amount of health that Isaac's persona has is related to how comfortable he is with that side of him.
??? is something he's horrified about, his emo (Eve) and rebellious (Judas) sides are ones he doesn't like, being strong and brave (Cain) is something he doesn't have the confidence for. His normal self is okay... But Magdalene is what he feels most comfortable with, hence the higher HP.
  • Makes sense. He also simply can't relate to Samson, who is the side that has a sense of anger and justice, a side he can't express under Mom. He feels most comfortable as a defensive, nurturing personality with Maggie's low speed and Yum Heart.

Satan represents Isaac's father.
When you finally fight Satan, he opens the battle with a distorted, demonic vocalization. Upon further examination, this is actually Mom's "Isaac!" line, just reversed and deepened. How does The Devil know your name? See title of WMG. In Isaac's mind, Satan represents his father. Dad's Key makes it clear that Isaac's father left their family. Isaac's mother presumably demonized her former husband, causing Isaac to hate him and apply a sort of "ultimate evil" tag to him. Now, Isaac's mother, being extremely religious, would obviously also apply the same tag to Satan, causing Isaac to link the two together in his consciousness.
  • This theory is given credence by the fact that in Rebirth, Dad's Key opens the room to the super secret boss, Mega Satan.

God never demanded a sacrifice. Isaac's mother was having delusions.
Some analyzers of the original Christian myth say that God stopped Abraham's hand when he was about to kill Isaac because God had never asked for a sacrifice, and Abraham was just imagining things. Following that line of thought, perhaps Isaac's mother in the game was also the same way. This would certainly explain why God stops Isaac's mother even though he asked her to do all those horrible things to Isaac. There were never such orders. Isaac's mother just went crazy from watching so much Christian TV.
  • Given the Halloween Update, she might have been manipulated by Satan.
  • Either that, or it's supposed to mirror the story as it is — God asked her as a test of faith. The reason He stopped her so violently was because she showed no remorse in killing her son, which showed she had faith in Him but no compassion for fellow humans.
    • It turns out that Isaac was the one having delusions…

The 11th Ending is a Time Loop from Future Isaac to be later found by his younger self in the 10th Ending
Thus making sure that its younger self will wake up from the illusion of salvation from his mother by the bible that God used or that he was making any progress at all by going on and on with killing his mother in self defense. In the end, he will realize that there is only death as a escape from the inevitable sacrifice by the hand of his mom, and God would not save him either.
  • This is sort of supported by the fact that XXX has the same nightmares as all the other characters, and that Mom still calls him 'Isaac'.

Isaac is an aborted fetus
His mother heard the Voice of God when she was pregnant, and sacrificed her unborn child. She's later been plagued by delusions of what she's done and what happened to him and where he is now, and the game is made up of her hallucinations.
  • Supported by The Wire, It Lives: Your Past and Future Self, and the 11th Ending.

Almost every enemy is a possible Bad Future for Isaac.
Many items end up making Isaac look like certain enemies. Or, alternatives, many enemies look like Isaac with certain items. The Seven Deadly Sins is where it's the most obvious, and with a few items from the Devil Room, he begins to strongly resemble The Fallen as well. Assuming the above WMGs are true, why stop there?
  • Confirmed, of sorts — Word of God has stated that every enemy is also Isaac. Of course, what that means and whether it's literal or symbolic is up to you.

Isaac is an abused, unwanted child, and/or the spawn of Satan — Either way, he wants to return to the womb and start over.
He's naked. He has no possessions. His weapons are all body fluids. Most enemies resemble Isaac. "It Lives" is Isaac as a fetus. Every form of Isaac is him dressed as a potential version of Isaac in the future. XXX/??? the Dead Baby — to whom Isaac reacts in absolute horror — is obtained AFTER YOU KILL ISAAC'S FETUS FORM. Every power-up mutates Isaac as well, representing future versions of him.

If we assume he's the spawn of Satan, it explains the offers and why he fights him at the end — it's a battle for control over his destiny.

In the end, Isaac has a showdown with Satan and finds a final chest… which cycles through all the personas he has taken and returns him to his room. What's in the chest, the same sort of chest that's found in the Womb? A chance to start over — Isaac can either keep his current life or try a new one (he chooses the latter).

Forget "Bad Future" — Isaac doesn't even want his Bad Present.

  • Isaac being the spawn of Satan, or some other kind of demon, is supported by the ending unlocked by beating the Cathedral. You fight Isaac himself, and the ending is Isaac looking into the mirror and seeing a pitch-black demonic version of himself.
    • And then it's all but confirmed by the ending you get by beating Mega Satan, where Isaac actually BECOMES A DEMON. However, the ending you get for beating the Lamb is more along the lines of Screw This, I'm Outta Here… at first glance. The endings you get for beating Hush and Delirium confirm that Isaac killed himself.

Isaac's mother abuses him and takes away his clothes because he crossdresses.
Either the "voice of God" thing was made up entirely, or her disturbed mind created it as a justification for extreme measures to prevent her child from being "deviant". Once she saw that he was still managing to jerry-rig costumes together, she decided the only way to stop him was to kill him outright.

Everything you play is Isaac's imagination.

Warning: Unmarked spoilers.

Okay, so, Isaac's mother does take away his toys and later thinks she has to kill him. He runs away in the basement and, while his mother is chasing him, hides in a chest and starts imagining things to pass time. However, because he lost his toys and his mother wants to kill him, Isaac can't think of anything happy, so his imagination (in other words, the game) is filled with his interpretations of all the nasty stuff he overheard from his mother's Christian broadcasts (or he is just a weird child, believe in what you want to believe). The unlockable characters are all imaginary friends he makes up for the fantasy as he plays, and so are the unlockable items.

The part when you beat Mom for the first time in the game is actually her closing in on him and searching for him. Then, the bible falls on her head, but that does not kill her. Rather, it knocks some sense in her head, and a The End... Or Is It? ending is actually just made unnecessarily ominous. Isaac's mom actually apologizes to him.

The ten mom kills that follow in the game is her returning Isaac's toys to him. However, he finds the imagination game to be a lot more fun than his toys were, so rather than playing with the toys, he uses them as an inspiration for some new elements for his fantasy. The final ending shows Isaac just returning to do what he did before: imagine.

Hey, does everything here have to be as grimdark as the game itself?

EDIT: Now that the Wrath of the Lamb is out, I guess I have to update this.

Isaac is growing up. He is getting now types of toys, new ideas, and is slowly nearing puberty. I say this because the items and bosses seem to be a bit more "mature" and different (see: puberty pills, stem cells, those faces + hearts, stuff generally not related to Bible, new rules, new floors, et cetera.) However, he realizes that he can beat all the bosses he thinks up, so he makes himself a new boss, the only one that might have a chance to defeat him: himself.

After Isaac does that, he tries to find new ideas and begins to realize that he is slowly outgrowing his game. He sees his devil form in the mirror as a lot more awesome form of him that, well, he just won't be able to be like anymore. That kinda correlates to the person playing the game realizing that he/she is running out of things to do.

Alternatively, Isaac is beginning to understand just how twisted some of the stuff he made up is.

Whatever it is, the final level, the Chest, is Isaac melding reality with imagination, giving himself the greatest, final challenge: Leaving his imagination game behind.

  • Including the toy he uses to hang himself?
    • Considering what monsters he made up, something like that is kinda par for the course.
    • I desperately want this to be true. I really do.
  • Perhaps Isaac is so obsessed with the imagination game that he starts spending all his time in the chest and begins to ignore the real world and his basic needs for survival. The Dead Baby is a warning from his mind that if he doesn't stop soon, he'll end up like it.
    • Wouldn't that explain neatly why all the rooms you explore all have the exact same shape as the chest?
      • COMFIRMED!!! Sort of. The entire game was Isaac's Dying Dream as he asphyxiated in his airtight chest!

To go with the above, Satan in-game is actually Isaac's dad
Basically, in Ending 13, we can see that Isaac's Dad left the family, and beforehand we see a lot of sad Isaac, so clearly there was a messy divorce, causing Mom to go mad from despair. Therefore, in Isaac's imagination, the only one that could cause such suffering is the devil.

First ending is the real ending.

This is similar to the above theory: As we can see, Isaac drew the opening narration pictures and the "Bible kills Mom" ending on the paper. The intro was Isaac recapping to himself what was happening, the actual game was hallucinations/imagination, and in the end he imagines himself a happy ending and draws it. But since it's imagination, that doesn't really kill Mom and she comes to the basement.

If/when the expansion is released, the Final Final Final FINAL boss will be God Almighty.
Averted, actually. YOU are the final boss!
  • Jossed in the remake. As far as we know, it's Mega Satan. And we still have yet to see the TRUE true ending.
    • Welp. We've seen the true true ending. And the Very Definitely True Final Boss is… an embodiment of Isaac's insanity. Mmmkay then.
      • And then that got upstaged by the Beast of the Apocalypse… which appears as some sort of Fusion Dance of Mom and Satan. It makes about as much sense as anything else…

Isaac has superhuman abilities, and when he grows up, he will become almost invincible. The family were mostly threatened by the mother's state.
Isaac, from birth, had to endure hardships. His mother's womb is really messed up. If he came out of that, alive, he has to be tough. After that, his father probably got sick as all hell. Possibly nymphomaniac of the millenium to keep that up. Most kids were broken before they even fully formed, leaving us the eyeless (taken out before they could fully form their eyes), headless (got so nasty a cranial infection that it had to be removed), and then genetic issues (the fly hives and the like being unable to physically take care of themselves). Isaac was so tough that he was able to resist all the problems, and his genetics were sound. Because he had to go through what is basically a warrior's challenge at birth, he was so much tougher for that, but because of that, he was too awkward around other kids because he never wanted to interact physically, so they teased him.

Isaac is the Antichrist, and the game is a Batman Gambit from God to make him into an Anti Anti Christ.
This may or may not tie in with the "in his imagination" theory, i.e. it might be images, dreams, or hallucinations sent to Isaac from God. Specifically, by enduring the horrors of his mother's excessive fundamentalism, he will be protected from becoming a Knight Templar when he discovers his powers; at the same time, fighting the monsters in the dungeon (and eventually Satan himself) both physically and spiritually gives him the means to fend off those who would do him harm, man or demon. Once he finally triumphs over Satan, God either erases the events from reality and makes them as nothing but a daydream (the memory of which will nonetheless keep Isaac strong in the years to come), or makes the dreams/images stop plaguing him so he can rest.
  • Supported by the ending unlocked by beating The Cathedral at the end of Wrath of the Lamb. You fight Isaac himself, and the ending is Isaac looking into the mirror and seeing a pitch-black demonic version of himself.
  • Note also that as of Wrath of the Lamb, The Devil Room will occasionally be replaced by an Angel Room. Perhaps God has decided that He needs to reach out to Isaac more, to ensure his success?
    • The boss fights in the Cathedral and Chest do lend some credibility to this. Throughout the fight, Isaac and XXX are being actively empowered by heavenly forces. And when you knock him down to 1/3rd heath and he gets angelic wings, he's smiling. It does seem to say that Isaac is, at heart, still a good kid.
    • So, where do the endings for the Dark Room and Mega Satan come in?

EVERYTHING is in Isaac's imagination, even his mother trying to kill him. His mother's been dead all along.
Perhaps Isaac's mother dies in her chair while watching her Christian shows, and the trauma of either seeing her die or finding her corpse drives Isaac crazy. Add in whatever madness that was being broadcast on the TV, and all those things combined would probably be enough to cause a little kid to snap.

Isaac's mother removed his penis.
His penis is visible in flashbacks, but not during the game. At some point before the voice's third declaration, Isaac's mother thought of another way to help free Isaac from sin.

The basement under Isaac's house, for some reason, is Hell
Kind of an obvious one, with all the aborted/stillborn/mutated/whatever siblings all over the place. Nothing here dies.

It's all in Mom's imagination.
Whether by miscarriage or abortion or accident or murder, Isaac is dead. Mom creates the events of the game within her head, starting with God's commandment that Isaac should be killed, to rationalize Isaac's death. Her fears tell her Isaac has fallen into Hell; her self-blame and self-loathing place her as a monstrous enemy of Isaac.

It's all a Xanatos Gambit of Satan
Mom never heard God´s voice. It was Satan, who tried to corrupt someone.
The possible outcomes:

-Mom kills Isaac, corrupting her soul.
-Isaac kills Mom, probably having collected enough "Devil-Items" to be corrupted
-A monster kills Isaac, Satan can try the same with another family
And Isaac battling the final boss is because he found out about that gambit and is seeking revenge.

Envy´s and Pride´s names are swapped.
Just think about it: Envy just floats around, smiling and being proud enough to not even attack, while Pride spawns bombs and energy-ray-things, generally being destructive, because he´s probably envious of what others have and wants to destroy it.
  • Actually, their names do make some sense. Envy splits into multiple enemies, and it is the only sin that can't truly be done by a single person. Pride, on the other hand, seems pretty confident for a boss who can only attack by either spamming bombs, which almost certainly involves hurting himself, or a diagonal attack, which no sane person would get in the line of fire for, as you can only fire in the cardinal directions.
  • Envy and Pride are Stealth Puns like Sloth being a lazy palette swap: he's beside himself with envy, and he's radiant (diagonal beams)/bursting (troll bombs) with pride.

Mom is simply getting a second child
When his Mom gets pregnant, he thinks she won´t pay attention to him anymore, thus the taking of his stuff. He begins to feel unwanted, believing his mother wants to get rid of him and tries to abort the fetus himself (It Lives!), even succeeding in his task. Then he realizes that he´d love having a new brother or sister and thinks, the dead baby would be alive. It would even explain the overabundance of dead babies in the basement!

Isaac's mother wants to kill him because of the father.
Note that the opening narration specifically states that Isaac lives alone with his mother, with no father to be found (and, indeed, a father would presumably attempt to defend him). With his mother's strong Christian roots, a divorce seems unlikely, which leaves two likely scenarios:
  • Isaac is a product of rape, and his mother goes insane and attempts to "protect him from sin" because she goes insane with the fear that he might turn out like his father,
  • Or Isaac's father and mother truly loved one another, and his father's death led to his mother going mad from despair.
    • The latter could indeed be possible, if this picture unlocked by beating Wrath of the Lamb with all 6 characters is any indication.
    • Ending 13note  shows that his father left the family.

The dead corpse in the shops is really Greed.
They have the exact same skin tone, Greed wears the noose cut off… It's like he watched you descend from the Basement to the Depths, where he may fight Isaac out of spite. Note, Depths 2 is the last level for a shop, and that tends to get replaced by Greed. The Womb and Sheol don't have shops. Probably tried to pull a You Have Outlived Your Usefulness on a potentially overpowered kid?

Isaac's Mom isn't religious at all.
The intro story and first ending are apparently narrated by Isaac inside his head, as each of them are his own drawings, and yet they are filled with religious themes and his mother's chanting (note that when she talks in-game, her voice is different, and she only says 'Isaac'), along with the bible killing her. Not only that, but there are many indications of child cruelty in-game ('Dinner' being Dog Food, as an example) which shows that his Mother has been deranged and abusive for a long time before her psychotic episode, despite the intro describing their lives beforehand as 'happy'. The religious themes are there because Isaac himself is religious (as people in desperate situations, such as an abusive childhood, tend to be) and the links to the Binding of Isaac story are just his naive attempts to justify his deranged psychopath of a parent. Mom bursting into the room in the 1st ending is just a stinger and not a genuine event, so the 1st ending leads straight into the 11th, where Isaac himself does the only thing he can think of to get away from her and locks himself in the chest, suffocating or starving to death. The game is his confused and terrified attempt to put everything together and remember his life as he waits inside the chest, hence the muddled religious themes and references to an abusive childhood in almost every aspect of the game.

Everything actually turned out fine in the first ending.
In the latest trailer for Wrath Of the Lamb, Isaac's letter to Guppy states that the basement is "different". This implies that he has been there multiple times. Perhaps Mom didn't actually intend on killing Isaac at the end of the first ending? For all we know, she knows Isaac's been to the basement and was offering the knife to him in case he went again?

Basically, ever since then, he's been making frequent excursions to the Basement and beyond. But why does he keep fighting his mother, you may ask? Well, that leads to my second WMG...

"Mom" isn't actually Mom at all!
It's a demon taking her form! Basically, Mom wasn't going crazy at all. Instead, a demon had captured her and disguised itself as her. It used Religious Fervor as an attempt to get Isaac to forsake it. And even if he didn't, there was still a chance of murdering a small child and possibly his mother. So, essentially, after Isaac fights the demon, his mother is freed, and she finds Isaac in his room, drawing his adventure down to preserve the memory of it. However, the knife was meant to attack the demon since she thought it was still around.

The demon keeps coming back, resulting in Isaac continuously going into the basement to fight it again and again. Eventually, he heads to Sheol to fight Satan, realizing he needs to destroy the demon at the source. The treasure chest Isaac entered at the end was actually the only way to escape, as opposed to Isaac essentially committing suicide.

Now, why would I make these 2 WMGs, you ask? Because Dammit, this story is just too fucking depressing.

Isaac's mother never tried to kill him, it's all made up by resentful Isaac
Mother does think Isaac has been "corrupted by sin" — because she saw the things he's been drawing, those macabre scenes (seriously, have a look at the pause menu) and monster designs. Immediately, she takes away his toys, which surely are to blame for Isaac's behavior. She has him read the bible instead.

Isaac is not easily placated. Inspired by the bible, he makes up several characters to play with. When he encounters the story of Isaac, whose name he shares, he starts imagining a story in which his mother wants to sacrifice him, but he escapes, regains things he used to play with before his mother took them away (and other things he thought that were cool), and defeats her with them. Since he's just a little boy, the plot is simplistic and somewhat nonsensical, but there are cool monsters and stuff!

He finishes the story, but still is bored, so he continues, not caring about the plot at all but just making up new cool items. Things also get a little Freudian...

At one point, he decides it's so fun, he might as well throw in him defeating Satan.

It is all a game... stay with me here.
Isaac is very young. One might assume pre-school age. Possibly even younger considering some of the many references to Number One and poop through the game. Too young to toilet train or fascinated by bodily fluids (including his tears of course) — possibly both — or just a case of a kid that is having trouble with the concept using the toilet yet (though you will see that I think the first as I continue). But he is also very smart. Possibly a young genius type that is too smart for his life experience. He is also possibly completely aware of his entire life from the point he was in his mother's womb with a brain developed enough to learn, to his current age… and his brain is only learning faster. A true wunderkind.

Being both young and smart, his short life up to now has been VERY traumatic to him. Being born (and remembering it all clearly) and having to cope with not being able to talk or walk or do anything but cry for attention (as his muscles refused to work even though his brain told them to and his body can't control itself because it was not developed enough) has been rather… distressing.

All of this has led young Isaac to be a bit of a delinquent youth at a very young age, and his mother is of a religious bent (though her zealous nature in her religion is all made up by Isaac, or at least exaggerated greatly) and she punishes Isaac by not sparing the rod (using a wooden spoon for a spanking, or maybe a belt on occasions when he has been extraordinarily bad). She may or may not be expressly abusive, but that is not important for the theory, and more than likely, she is not as abusive as one might see based on Isaac's imagination, she is simply punishing a bad kid and trying her best to hopefully turn him into a kid that is good.

Being so smart did have some social struggles that were unfortunately brought to bear for poor Isaac.

One, his father did leave. He could not cope with a child that was smarter than him at such a young age (or at least showing signs of being smarter) and/or he simply did not understand his son. Perhaps he was simply an ass-hole dad too; it doesn't matter, the point is, he left. Two, Isaac's vastly superior intellect compared to anyone else made it hard for him to identify with children at a day care or pre-school of his own age, and anyone that he might have been able to have some form of conversation with would have been too old to try to talk with the small child. Plus the fact that even if someone had wanted to try and converse with him, his young age made his life experience too limiting to have any real conversations about anything "real".

Isaac was kept at home as a result of the awkward nature of his interactions and his generally anti-social standing with other children.

This along with a chest full of toys — including a copy of a role-playing game of some sort, and the requisite dice — has led Isaac to create for himself a game to try and bring the ideas buzzing in his head and his own emotional struggles into a more cohesive whole. Unfortunately for him, he is not that good at writing yet and can only draw in a crude manner. Obviously he only has access to crayons as well. He has created alternate egos and imaginary friends along the way and incorporated these into his little game.

Many of the items one finds in the game are simply household items or elements of Isaac's fantasies and imaginings being brought into the fold. His brain is still that of a child despite being so smart and so the rules are also always in flux and difficult to pin down for him. He makes up some as he goes (play-testing over and over as anyone might) and some he writes down when he can figure out "the math" of it. Since he has not been to school yet, his math is often wrong (leading to many inconsistencies in the game and some just plain missing or incorrect).

The game has even been played out in his basement in a live action format, hence the addition of things such as spiders and flies. But of course a simple spider (or fly) is not a very good enemy as one levels up, so he creates many variations on them in more powerful forms, including boss monsters with themselves having even more variations.

The many elements in the game that seem abusive, or religious, or sadistic, or masochistic are simply exaggerations of Isaac's upbringing with his mother combined with his own 'too smart for his own age' brain and imagination. Truly there is nothing sadistic in his imagination, he is simply trying to make a fun game to pass the time in his loneliness. The true tragedy is that he is simply a lonely boy who does not play well with others due to his youth and smarts. Something that will change as he gets older, of course, but at this point in his life it all seems hopeless (hence some of the themes in the game).

The setup of the game is such because of the games Isaac has played in his youth so far on his Nintendo Gameboy. One day maybe he will make his own game, but of course he does not fully understand how to code yet, so right now the game is pen and paper (and so far only a few pages worth in crayon… mostly pictures since even his intelligent brain gets distracted like a child and he ends up drawing a cool picture instead of writing down some odd rule he is already struggling to get from his brain to the page).

As to some of the themes of animal cruelty or eating animal food (or rotten food) in the game, well, he is a small child, probably had a pet or two, and after they died (or an accident happened) Isaac might have done some exploratory post-mortem experiments on the dead pets. He is not disturbed (we hope), just curious. When it comes to gaining health from the food, he has probably had some of that food before… again, still a small child.

Finally, a note on all the dead baby references and Bob (Bob's Rotten Head, etc). We do not know exactly what Isaac found when he went into the basement. And the primary theme is of his toy chest (a place of safety turned into a horrible nightmare) all starting in the basement...

When Isaac went into the basement for the first time to play his game in live action, he found (among other simple and normal things) something very bad. He of course did not know it was bad, but it traumatized his small brain and caused him to retreat to the safety of his mother (as evidenced by The Womb) and fight his fears with a LOVING mother who told him it would all be okay.

In the end, he ended up back with his toys, in his room, with that secret entrance to the basement still there... Bob's Curse forever in the back of his mind. And so his game is both a fun enjoyment for a boy that will one day become a game designer (or a serial killer, we hope the former) and has all the elements of his life up until now. Write what you know, as they say.

Some after thoughts about the "main bosses" of his game.

Mom is represented because when Isaac found "Bob" in the basement, his mother was both terrified for her son and furious he had done something so foolish as going down into a place he did not understand. (She of course had that all cleaned up and taken care of and possibly even locked the door Isaac found in his room... which Isaac of course has a key to, hence the keys and locked doors figuring so prominently throughout the game.) Her fury scared him until after he understood it was not directed at him, but that doesn't stop him from liking the idea of the giant foot of Mom smashing down on his player character! She did, after all, kick down the basement door to get at whoever was causing her son to scream bloody murder (with knife in hand)!

Satan (added in the Halloween update) is... Satan. Isaac's own Halloweens are not filled with the fun costumes and candy of other kids because his mother doesn't believe in that sort of thing — hence there is no candy in the game... what kid would NOT add candy in a game of their making if they had candy a lot? So after his mother's explanation of why they do not celebrate Halloween, Isaac incorporated the horrible beast of Satan into his game.

Mom's Heart and It Lives are a little bit weirder and difficult for me to explain (or understand) but may be due to his experiences at birth and the fact he remembers it all. Something most of us "normal" people forget of our past. And for good reason.

Isaac himself, and why in the Cathedral? Well, what better boss to have as the epic end boss than yourself? And what better place to have as the final dungeon than not a dungeon at all? After all, if you were going to make yourself into a boss, would YOU live in some horrible place, or a big beautiful cathedral?

Finally, Blue Baby/??? and the Chest. Isaac has been traumatized by his experiences in the basement with Bob and sometimes his fears lead him to hide in his toy chest. It is a safe and secure place for him to hide in. This has led him sometimes to a lack of air. Not completely, of course, as his chest is not air tight, but he has had trouble breathing on more than one occasion in there. With nothing to keep him occupied in the chest but his own fears and memories and imagination, he has created the ultimate "boss" in the ultimate dungeon. His own toy chest (evidenced more so that it IS a "toy" chest by the fact that you gain four items on entering (with enough keys that is)) and his own dead form. Death has of course been explained to him at least once if not many times (Bob, Tammy, Max, and Guppy to name a few) and so he knows that "death is the end" and that no one comes back. But hey, he is smart and creative and so before even getting to read or watch stories about zombies he has created one in his own game! And better yet... you get to PLAY as a zombie! WOO!

We will see what kinds of themes and dungeons and bosses enter the next stage of Isaac's little game in Rebirth. And if this little theory of mine holds true with those themes.

  • Well, the Dark Room is a stereotypical final dungeon — it's a dimension of pure darkness, for crying out loud! I dunno what the Lamb is — probably some demon trying (and epically failing) to pass itself off as Jesus Christ Himself. (Seriously, the upside-down cross on the forehead isn't helping its case.) As for why it's fought after Satan, your guess is as good as mine — maybe seeking revenge against the guy who offed its boss. Mega Satan, on the other hand, is clearly Satan gone One-Winged Angel — because when Satan himself isn't enough of a challenge, well, maybe it's because he was holding back? Then Hush is asphyxiation, and Delirium is Exactly What It Says on the Tin.

    • You were in the ballpark with this idea. It's just a bedtime story Isaac made up with his father to help him sleep.

The story, especially with Wrath of the Lamb, is a metaphor for Isaac's coming of age.
Isaac is beginning to enter his teenage years, probably coping with depression, and the entire game is allegorical. To wit:
  • Isaac's mother is not abusive, nor attempting to kill him. This is a metaphor for increased tension between the two; as a single mother, she gets the brunt of his depression, outbursts, etc.
  • When fighting Mom's Heart, he is in fact hurting her with words, possibly via an argument. Similarly, It Lives may be a metaphor for either suicidal thoughts, or claiming he wishes he'd never been born.
  • Puberty pills can be found after Wrath of the Lamb, suggesting that Isaac is changing more and more.
  • All of Isaac's different personas aren't "playing pretend" in the traditional sense — rather, he's grappling with his identity, and trying on several different personas (Eve is a stint with goth/emo, Cain and Samson with being "badass" and/or a delinquent, Judas with being cool and classy, and Maggy with being cheerful and "normal"). He's likely also grappling with gender issues, which his traditionalist mother either doesn't understand, can't accept, or doesn't even know about.
  • There are three different final bosses with Wrath of the Lamb, all potential outcomes to a crisis of faith as he questions his beliefs. Defeating Satan represents Isaac staying a devout Christian, and possibly making peace with his mother. Defeating Isaac represents Isaac coming to terms with sin, and embracing agnosticism/atheism/a non-Christian faith.
    • We haven't accounted for Blue Baby here. And in terms of the new endings in Rebirth, well, defeating The Lamb probably represents Isaac pulling Screw This, I'm Outta Here on his mother, and defeating Mega Satan probably represents Isaac deciding Then Let Me Be Evil after a long, depressing struggle with the dissonance between his own human imperfection and his religious faith.

Isaac suffers from Dissociative Identity Disorder.
First of all, if the majority of the game is taken at face value, Isaac has clearly had an abusive childhood — the sort of experience believed to foster DID. The other characters are, in fact, alternate personalities, who fight his mother in his place as a coping mechanism. In the Twelfth Ending, whichever personality takes down Isaac is, in fact, subsuming the real Isaac. Assuming Isaac beats The Cathedral, then a Split-Personality Merge results instead.

Isaac's Dad abandoned the family a long time ago
In Wrath of the Lamb, you can pick up an item called Dad's Key. This item unlocks all the doors in any room, and is primarily designed to allow you to run away from conflict.
  • Confirmed with ending 13.

Conquest is, in fact, War having taken a level in badass.
Of the original Four Harbringers of the game, War is almost always considered the easiest to fight — this in spite of being, you know, the personification of ALL COMBAT. Conquest only appears on the later levels, either replacing War or even after defeating him, and the distinction between Conquest's and War's domains is very minimal (hence why Conquest is replaced with Pestilence in most modern depictions of the Horsemen in the first place). Finally, their abilities are very similar:
  • War is the only one of the "Harbringers proper" to charge multiple times in a row, and will often charge after a standard attack. Conquest has the unique ability to create multiple bodies to charge at once.
  • War can raise his horse to the sky to summon troll bombs. Conquest can also raise his horse to the sky, summoning pillars of holy light.
  • On a more meta level, when Conquest appears, you may receive the boss intro screen for War instead. Glitch, or HINT?

Completing and using The Polaroid brings the Stable Time Loop, and Isaac's suffering, to an end.
Completing The Cathedral with six characters unlocks an item called the Polaroid. Take it into the fight with Isaac, and rather than fighting him, you instead fight ???/Blue Baby. By the end of the fight, he will rise in a column of light and Ascend to a Higher Plane of Existence, just like Isaac did in his previous fights with him. After this, Ending 12 makes a lot more sense. His previous suicide attempt failed and turned him into Bluebaby. However, he managed to free himself and send himself to heaven by defeating him. This sinks in right after he does so… and he then realizes that he must kill himself and turn himself into Blue Baby once more to get his redemption and peace.

He refuses to leave without a ten-inch saxophone, a twelve pound bowling ball, a glow in the dark snorkel, and a chainsaw, because they give him super powers. Like the ability to survive a plane crash.
  • He didn't survive the plane crash because of superpowers, it was because he had his tray table up, and his seat back in the full up-right position!

Isaac is Isaac Clarke
Being very young during the events of this game, he is quick to block it all out of his mind after it's over. However, the experience he gains from fighting all of these horrors stays with him into adulthood, enabling him to instantly Take a Level In Badass when he has to fight Necromorphs.
  • We do found out in the expanded media that Isaac Clark's mom was sucked into Unitology and his father left when he was really young. So if we assume that his mom squandered their money on Unitology, went crazy over time as she was hearing voices in her head (the voice of Altman to her), and tried to kill her son for the purpose of Convergence, this theory checks out.
    • You'd think he'd remember Unitologists' fatal weakness to Christian Bibles.
  • This would explain why Isaac is so good at dealing with markers; he's been though this sort of thing before. However, he either does not fully remember it, or thinks it was a dream, but nevertheless, he has experience with surviving a Body Horror-infused world.

In the true ending, Isaac has become convinced that his mother is right.
The book he's reading as he hides from his mother in the chest is the Bible, and he's been tearing out pages to write down his adventures on the back — and reading Bible stories, which terrify him even more. When Isaac goes down to Sheol, he's sinking deeper into his fantasies and deeper into terror of his monstrous mother; the fight with Satan represents, at once, the end of his fantasy and full integration into it (read: the multiple personalities fusing and hiding in the chest to "escape his mother", suffocating him). When fighting Isaac, Isaac decides that his mother is right: he is corrupted and unworthy of life. This is represented by his looking like a demon in the mirror. When he eyes the chest, he has decided to hide in it and suffocate himself to death.

Neither God nor Satan demanded Isaac's mother to murder her son.
The voice at the beginning telling his mom that her son was corrupt belonged to her husband. After unlocking Ending 13, it shows a series of photos from Isaac's life: Isaac and his happy parents, Isaac dressed as Magdalene and his still happy mother, Isaac's parents without him, Isaac sad and alone, Isaac's shadow in the shape of a demon, Isaac crying naked by the chest, Isaac's mother attempting to kill him, and Isaac and his mother watching his father leave.

Isaac's mother was fine and even supportive as her son took on separate identities. She loved him regardless of what he decided to be. His father, on the other hand, didn't. He was the one telling his mom that Isaac had become corrupted and needed to be saved (with this in mind, it suddenly makes sense as to why she also takes Isaac's clothing during her cleansing montage). Eventually his demands became more severe until the choice came down to Isaac or his father — "to prove you love me above all else." His mother then did try to kill her son, but was stopped at the last moment not by the literal bible, but her faith. Isaac's father, either disgusted at what his wife tried to do or by her accepting Isaac's "sinful" ways, leaves.

This idea makes another theory more prominent: the entire game and fight against Satan and himself is all in Isaac's head. After being mentally scarred by his mother trying to kill him, his father abandoning them, and everything they'd said to imply it was his own fault entirely, Isaac locked himself in his chest with all his toys and clothes. The game is his dying mind scrambling up his memories, hating himself, and attempting to justify the actions of everyone around him. Only by bringing the polaroid to ??? (his dead self) in the Chest does he begin to correctly remember what actually happened, but by then it's too late and his real memories can only flash before his eyes.

  • Based on a recent interview with Edmund, this seems quite likely. Specifically, his mother's side of the family were fairly permissive Catholics while his father's side of the family were fundamentalists of the "Dungeons and Dragons are Satanist indoctrination!" sort, and he mentioned that these experiences heavily influenced the creation of the game.

Isaac's father leaving in the True Ending is a metaphor.
If we assume that most of the game is metaphorical, and that most of the photographs are as well — e.g. that Isaac wasn't really fighting against Satan/his own inner sin, that his Mother never really tried to kill him, etc. — then why not the final one? In actuality, Isaac's father died, and his mother (though not nearly as abusive as she's portrayed) grew cold and distant due to his loss, one of the few acts of kindness she was still able to show being to reassure her son that Daddy was in heaven now. And if all kids go to heaven, there's a toy chest right there that might be airtight...

Isaac did not succeed in suffocating himself in the toy chest.
When you kill Isaac, it represents Isaac deciding that he is indeed corrupted by sin and should bring himself out of the world. However, there are two primary reasons for this theory: One, it's a goddamn toybox! The things would surely be childproofed. And two, the True Final Boss is the Blue Baby, representing Isaac's death by suffocation. In the final ending, you kill him, and in doing so, Isaac decides that though life is hard, those happy memories are worth it, and he'll persevere.
  • Note that in order to fight Blue Baby, you have to obtain The Polaroid, a memento of those happier times. Without it, Isaac gives in to despair — but with it, he realizes that there's still hope.

Or gets bored of waiting to suffocate in a toy box that isn't airtight, whichever.

The game itself is specifically designed to be a metaphor for a religious text.
To wit: It's a game that relates a tale of a child whose parent(s?) has/have it in for him, and is forced to murder them for his own well-being, and that takes several elements from Abrahamic mythology (duh). However, what really cements it is this page.

The game is intended to spawn wild theories. Its ambiguousness and heavy use of metaphor point to this, because this allows people to interpret it in any number of ways, just like a religious text. You can interpret the whole game as a metaphor, or bits as metaphorical, or damn near nothing as metaphorical! You can decide that Mom is in fact abusive, or that it's an exaggeration or a construct! Edmund and Florian made the game with the exact intent of spawning a Talmud of sorts.

Another theory on the meaning of the game
The entire game is a metaphor about how Isaac preserves the basement after he is chased in it. The photos show a happy family, and things aren't necessarily in order. Everything about the game is Isaac's view. The enemies in the basement? How Isaac interprets what he sees down there; either stillbirths or horrific dolls. Mulligans are ones infested with flies, other humanoid enemies represent other things, such as ones without eyes, or ones with only a functional head. The flies, mostly friendly to Isaac, come in two variants. A housefly, which Isaac is used to, and enemy flies. Red flies are mosquitoes, and bite him when they land, black flies are houseflies, harmless so Isaac sees them as friends. Pooters and such are wasps, but rather than stinging him, they shoot. His powerups are his toys, and between coping with the horror of his basement and so many odd things, and seeing his toys again, his scared mind decides to play games. After the first incident, Isaac got curious and kept going down there, seeing as his mother kickstarted it, he saw her as his "boss" when, in reality, she calmed down after her first rage, and saw what she had done; letting Isaac play downstairs, letting him look, but if he got too scared he would run back upstairs, I.E. game over. After 10 times, he becomes so confident in his abilities he starts to play a new game with them.

Each aspect of Isaac is different. Original Isaac was the one who was running; Eve is the manifestation of his depression, that he is weak and needs pain to keep going, remind him of who he is. Maggy was his imitation of his mother, and had the most positive outlook at life, with the most health as he believed God was with him, just like mom. Judas was his belief that he couldn't be trusted, once again low health, but felt that he had power in his own decisions, the high attack. Cain was the belief that he killed his brothers by being alive, so he "stole" their life from them, and he was lucky to be alive, the highest luck. Samson, his final one, he felt empowered, he knew how to work around his "enemies", the more there were the more powerful he needed to be for each challenge ahead of him. ??? was his cautious run, just checking around for stuff, why he is so willing to go upstairs.

The mirror ending shows his fear about being what his mother had believed, hence his restored faith in his mother after she got hit with the bible. After fighting the Devil, he realizes that he had become so engrossed in his game that he's become violent, seeing as evil is supposed to have violent urges, swatting flies in the basement. The heaven ending, which canonically comes first according to Word of God, is him seeing what happened, that he had given himself to heaven, but did so violently, and solved his problem as such. The chest, when he is locked in it, he finally sees, in a moment of reflection, that it is he who has to decide how sinful he is, as he knows who he hurts, finally seeing the pictures again, the sin his mother and father had done so innocently, letting him come out of the toy box stronger in person.

The Blue Baby is... Isaac from the fifth ending!
What? Ok yeah, I'm three final bosses too late for this to be a real theory, but come on. Who are you to say which endings are canon?

The first run of the game always ends with the reveal that it was a story he was illustrating, but then Mom bursts in and tries to kill him for real. Because he subconsciously associated his mother's overzealous Christianity with her increasing neglect, he incorporates Christian symbolism in with various monsters he dreamed up for the story. As things go on, elements of past drawings incorporate themselves into his story, particularly his earlier works. At some point, he realizes what happened and decides to draw his mother aborting him in an attempt to prevent this all from happening. After killing himself as a fetus, he goes on to either heaven or hell. If he reaches heaven, he must destroy himself as a consequence for the paradox he created before. Afterwards, he either ceases to exist, or, if he has the Polaroid, convinces himself it was All Just a Dream, negating everything that happened.

We're going to see a big rise in numbers of kids called "Isaac".
Previously famous Isaacs were all stuffy old scientists like Newton and Asimov. Now a generation of gamers will look at a newborn child, bawling with its oversized, toothless head and think "Hey, it's Isaac!"

Sister Magdalene.
Just a small one, but something I think a lot of people might have looked over. In the game, you can get an item called "Sister Maggy" which is essentially a fetus, possibly an aborted or stillbirthed one. Now, one of the first characters you unlock is a "Magdalene", which is basically Isaac in a wig. Now note that most people call Magdalene "Maggy" as it's shorter. It's very possible that Magdalene was a sister Isaac was going to have, but who was stillborn. In an attempt to please his mom, or perhaps thinking himself responsible in some way, he dresses up as Magdalene by putting on a wig. The reason Magdalene has more heart containers at the start as well as a healing item, is that he feels good about himself trying to "atone" for it, as well as the healing item might be more metaphorical for healing the damage done to his mother and the family. If we want to stretch this further, this might be why his father left the family, as we can see in the 13th ending. This might be further evidenced by the 13th ending, in which we can see Isaac dressing up as Maggy even before his mother went insane.

Isaac's mom remarried.
Another theory taking the game from a symbolic perspective. After Isaac's father died or left, whichever it was, his mother managed to find love again. However, Isaac felt like his mom didn't care about him any more, because she spent all her time with this new and strange man she loved "above all else". His new stepfather was stern and restrictive, and especially disapproving of Isaac's tendency to dress like a girl. So, he expressed his feelings through his drawings, writing a story about his mom's worship of this new man and how, he believed, she would kill him if "her god" asked her to.

Guppy is the key to EVERYTHING.
Isaac's will leaves things to Guppy, a cat who is clearly dead since you can find various parts of him during a run. If you find 3 parts of him, Isaac transforms into an anthropomorphic version of Guppy with powers. Now consider that a lot of Guppy items show up in the Satan rooms.

Isaac had a cat named Guppy who was legitimately evil. Eventually Guppy died, but young Isaac never sort of accepted it (being a baby and having no concept of permanent death yet). He was delusional that his cat was still alive and keeping its evil essence around by treating it as if it were. God noticed Isaac's affection for the demonic cat and how dangerous it could be and told his mother of the corruption, leading to the plot of the game. Satan, meanwhile, tempts Isaac with giving up his soul (his life hearts and soul hearts) to be with Guppy again by offering him parts. Attaining enough parts causes a profane transformation where Guppy and Isaac become one, granting demonic cat Guppy access to our world.

Isaac is Infected.
The trap door to the basement in his room is a gateway to the Linear Maze, which ends somewhere in Chessboards Five or Six. The trip gave him an initial Twist of ballistic tears, and whatever power-ups he gathers are further Twists, reflected in his increasingly mutated appearance and expanded abilities. The monsters he's having to deal with are either Actors playing out their roles in a Caretaker's drama, or (in the case of the Mulligans and Hivers) other people who are lost in Wonderland and too insane to find a way back to Chessboard Zero.

Isaac's Mom, in this theory, is being manipulated either by the Army of No, or one of the Caretakers' lackeys impersonating God. The boss fight against her is actually against her Shadow after its tormentors have had their way with it.

  • Satan is a Caretaker, and Boss Isaac and Boss Blue Baby are Isaac's own Dissociated Shadows.

The whole game is Isaac coping with his sister's death.
The theory is best summed up with this handy graph. The only canonical endings are 12 (Isaac contemplates suicide), and either 11 (Isaac goes through with it) or 13 (Isaac decides against it). Note that beating Satan (committing suicide) is easier than beating ??? (overcoming grief).

The game is in Isaac's head, but still goes to reality for some of the endings.
Most of the game is in Isaac's head as he travels through the basement fighting monsters that he imagines. He writes down his adventures as the different personalities he has, representing the characters. Most endings represent him taking toys out of his toy chest until the tenth ending, where he realizes that if he continues for too long he'll cause himself to die because of the lack of bodily needs, thus he is incredibly scared. In the 12th ending, he reads the bible and, with the realization and shame that he is so sinful, imagines himself as a demon. In the 11th ending he goes through all his personalities (and a demon to represent his sins) and ends up locking himself in the chest to get away from his mother. The reason he tried to do so is because he no longer knew the difference from reality and "the game". Something to note is that ending 12 comes before ending 11. However, in the 13th ending, Isaac finally remembers all the good times he had, and also the sadness of his father's death, from the photos in the chest and as such, decided that suicide isn't worth it.

Isaac's last name is Jogues, and the other characters and him are all martyrs.
Isaac Joques, the real-life one, has been a martyr along with other martyrs for dying for their faith for preaching Christ's love. Now what was the unlockable credits theme for beating the game 10 times and getting Blue Baby?
  • Jossed. As revealed by Four Souls, it's Moriah.

The Voice in the beginning is Las Plagas.
Think about it. In Resident Evil 4, you can find small human bones in the first area; implying that the violent nature of Ganado led them to murder children.

Isaac's mom was one of the first victims when the Plagas sample was brought back by Ada, hence, Ax-Crazy behavior.

Isaac does not survive the initial fall into the basement.
One of the traumatic memories Isaac can see between levels is falling through the trap door, then hitting the floor below in a broken, dead/dying heap. Isaac is Dead All Along from the very start of gameplay.
  • You're kinda right. The part about being dead all along is right, but none of the game actually happened and it's just a Dying Dream.

Cruel Sadist is Isaac's mother at a young age.
This one was inspired by Edmund's posting on the BoI Remake page's posting about his involvement in creating a MtG card.

Isaac's mother was never a well person between the ears. There were several unexplained sadistic and kinky serial killings in the city she was born in. After getting too... enthusiastic with one of her victims, she ended up pregnant with Isaac. The realization rattled her, and she fled to a small town in the middle of nowhere and took up religion to try to suppress her urges. During her pregnancy, she ended up really letting herself go, in a spiral of self-loathing and guilt. Fastforward about 7 years and her willpower has been flagging as the isolation and her guilt has been deteriorating her already frayed sanity. And thus the start of the game.

The game is not just allegorical to the Biblical 'Binding of Isaac...'
But it is also allegorical to the Book of Job. Isaac was originally a happy young man with a healthy relationship with his mother, pleased with the world around him and content. However, because of what lurks beneath his house, God and Satan both know that he could accomplish many things if pointed in the right path. So to test him and his character, God and Satan make a wager, with Isaac and his mother at the heart of it. They use her to take away Isaac's worldly possessions and shatter his happy lifestyle, and then force him to go down the path into the basement to save his own life from his mother.

From there, three things can happen: Isaac can go the holy and pious route, becoming the second coming of Jesus (the Isaac seen in the Cathedral), or go down a dark path and become the Antichrist (in time morphing into the abomination called 'Mega Satan'). Or he takes his destiny into his own hands and commits suicide, depriving both God and Satan of their wager and becoming the shriveled, hidden, and decrepit Blue Baby. (Or he just runs the f*** away from the ruins of his old life.)

The voice that told Isaac's mother to kill him was Samael, the dark god of Silent Hill.

This game is a Silent Hill game in disguise. When Isaac falls through the trapdoor into the nonsensical basement that changes shape every time you play, he's actually falling into the Otherworld, hence the disturbing eldritch abominations that seem to mirror Isaac's own fears and sins. There's also all of the multiple endings, which is a shared trait of Silent Hill.

The ending you get for beating The Lamb may actually be the Golden Ending.

Now, you may be wondering, how the *** can an ending in which a child goes missing be considered a Golden Ending?!? Well, let's not forget that Isaac's primary caretaker — namely, his mother — was trying to kill him. So, if Isaac is missing, that may mean that Isaac may have actually succeeded in escaping from his mother with his life intact, something which none of the other endings really imply (though this does beg the questions of where he goes next, and at what cost did he escape?) If Isaac managed to get himself taken in by a good family, which would actually take care of him, then this is definitely the game's Golden Ending.

On the other hand, it's also entirely possible that Isaac is "missing" because he's hiding in his toy chest (see the Cathedral, Sheol, and Mega Satan endings). And, also, Isaac is a young child who would probably have difficulty fending for himself on a long-term basis, so even if he did escape, unless he finds a foster family, he may be quite screwed. And this is assuming that whoever finds Isaac doesn't just send him back to his murderously insane mother. So, basically, Ending 15 could be the Golden Ending, but it could also be yet another bad ending in a game with no good endings whatsoever. (The Chest ending explains absolutely nothing about what happens to Isaac afterwards, so it doesn't count.)

Isaac's house was built over The Trap Door
Not much more to say, both The Trap Door and this game have a trap door that leads to an underground tunnel system full of monsters.

Isaac grows out of this fantasy...and eventually grows into another

It has been stated that not only are all the player characters Isaac, all the enemies of the game are ALSO Isaac. So what are we to make of the Gemini boss, AKA the player character from Time Fcuk being one of the enemies?

It has also been stated by Edmund McMillen that there is a greater connection to BoI and TF than currently realized, perhaps it's that they actually share a protagonist?

The PC in Time Fcuk is never actually directly named, the lump on him that seems to voice his own darker thoughts is named Steven and in one of his messages to himself he starts to wonder if he actually is Steven after all.

In a sense he is, the tumor-like growth represents the darker self-hating side of him growing on him once again years after he put his coping mechanism that is the dream world of Binding of Isaac behind himself. The game itself is his new attempt to escape reality in a different enough way that he doesn't feel like he's childishly regressing, also taking on a more cerebral puzzle-solving tone to make himself feel more grown up.

Azazel is Isaac's demon form seen in Ending 14 of Rebirth.

They look very similar, and Word of God says that all of the player characters are Isaac...makes sense.

The final boss of the Rebirth expansion will be Azazel
.

Given that we've fought Isaac himself and Isaac's corpse, it makes perfect sense to fight his demon form.

  • Jossed. There are two new major bosses: Hush, who seems to be a suffocated Isaac or ???, and Ultra Greed, the final boss of Greed Mode.

The game is a compilation of Isaac's nightmares due to the abuse of his schizophrenic mother.

The symbolism in the game carries two major themes: The obvious religious symbolism from Isaac being raised in a VERY fundamentalist household, and the symbolism of decay and abuse. The later is given in the form of very old and neglected food and even poop being powerups for health, various items that increase speed leave marks on Isaac, and it's clear he fully understands a lot of religious symbolism from various Bible stories, tales, and stigmas. We've seen that Isaac is a very imaginative child who enjoys dressing up as various characters (See: Flashback with the Magdalene wig.) and enjoys drawing. His toy chest is where he keeps a lot what he plays with and given what he finds in each one at the various endings, this includes drugs he finds around the house due to his mother's inability to keep track of them. The events of the actual game are nightmares Isaac has when he hides in the crawlspace under his room. The transition screen between levels shows him cowering in that same spot regardless of where you are in the game which hints that he's not actually moving anywhere, but letting his imagination and trauma from the abuse mix into horrific nightmares.

The fact that various items belonging to Mom are found throughout the game show that Isaac is aware of these things, including a multitude of pills, injections, and chemicals. This leads to two potential ideas: Either Mom is a pill addict and this is the cause of her insanity and hearing voices, or she is schizophrenic and takes these pills to try and mitigate it, but due to her rather neglecting nature, she can't keep track and leaves them all over the house. Religious preoccupation (An obsession with religious thoughts and standards as a coping mechanism) is a common byproduct in schizophrenic patients, so this might tie into her strict religious standards which are being reinforced by her voices. This might also explain why the father may have left the family as shown in some of the endings.

Isaac is Calvin's Darker and Edgier cousin and the game is the way his parents get him to eat.

What if the health powerups aren't actually dog food, spoiled milk, and old beans, but Isaac just feels that they taste that way?

So, Isaac is a picky eater, and he doesn't really like the food his parents make (and if Isaac's parents are anything like Calvin's, he's got good reason to). Occasionally, he flat-out refuses to eat. So his parents asked what they can do to make him eat, and he told them that they could play a game. Thusly, the meal-based Health powerups are Isaac's parents successfully getting him to eat his breakfast/lunch/snack/dinner/dessert. However, Isaac has gone to some dark places, and so the rest of the game and all the symbolism is Isaac's dark imagination showing off its darkness. His parents take some inspiration from his imagination and use it to create a new game every time.

That makes the BASE MENT seed Isaac's parents' ultimate triumph, since after the Item Pools are exhausted, the only thing left is Breakfast, which is why Isaac's parents played this game with him: to get him to eat his meals.

The game is a huge struggle over Isaac's destiny as the Anti-Christ.

So both Satan and a representative of God occasionally pop up in their respective rooms with items. Satan tempts you with collectibles for the price of life, while God gives you them for free. An Angel Room only appears if a Devil Room appeared before and Isaac resists the temptation. God was watching, found that Isaac rejected Satan, and decided to help. If Mom really was ordered by God to kill Isaac, then not taking a deal with the devil proved to God that Isaac is capable of redemption despite his... inner self. If Mom was just insane, then God simply decided to throw his hat in the ring to save Isaac. This line of logic implies that Isaac really did escape should he beat The Chest, considering that particular ending.

However, should Isaac rebel against God and attack the angels, the angels carry the key pieces to Mega Satan's domain. As mentioned in the main article, the two angels join the fight in a much darker form, implying that their failure to prevent Isaac from reaching Mega Satan was punished and they fell into Sheol. Despite their form, they still hope to rise again in God's favor, and so attempt to kill Isaac. Given the player's skill and luck, Isaac beats them and Mega Satan (and everyone else).

By that moment in the game, you've probably picked up a couple dozen collectibles, making your character completely unrecognizable from a naked crying boy. Isaac is now completely corrupted by the experience. The reason Satan turned on him is because he started to realize that Isaac was becoming too powerful to control, and rightly so. Isaac destroys Satan entirely, and truly becomes the Anti-Christ, or at least something like it.

So why the tears, the monsters, and the fighting? It's almost all a test, to see what kind of person Isaac truly is. It isn't exactly a battle in the center of the mind. Isaac is transported to an alternate realm partially made up of his own subconscious, evidenced by Mom's grotesque appearance and the constant references to Isaac's broken childhood and household. The collectibles are a combination of granted gifts and inherent powers that Isaac discovers in himself and out in this mysterious realm. He gains control over them, then chooses his fate. Should Isaac fail entirely to either escape or kill Satan, then he snaps back from the very real fight to die alone of suffocation, hence why The Lost floats away from the dead Isaac's body. ??? and The Lost are two separate existences, the body and the soul. God takes pity upon Isaac and grants Isaac a chance, using both, to redeem himself. They are, of course, much more difficult their time around, as Isaac loses life and corporeality. And Isaac may still choose whether to escape or overthrow Satan.

Greed will be made a playable character in a future expansion.

Greed is probably the most popular of the Seven Sin bosses, even receiving his own mode of sorts in Afterbirth. Also, the ending you receive for clearing Greed Mode implies that Greed is yet another aspect of Isaac. In this case, he's what Isaac becomes when he hangs himself after being trapped in a secret room by a cave-in. On top of that, the ending ends with Greed smiling — happiness that he'll soon get his day?

  • CONFIRMED. Maxing out the Greed Machine now unlocks Keeper, a playable version of Greed.

Isaac is actually biologically female

Well, he has female personas, a penis isn't visible in-game, and in one of the loading dreams in Afterbirth, the little dot between his legs actually falls off.

Isaac is stuck in a "Groundhog Day" Loop.
Think about it. Almost twenty different conclusions, a few of which have Isaac definitively dying. The game's Rougelike nature. The two different paths partway through. Isaac is stuck in a loop of sorts where he is able to choose his persona and the specific experiences he has are always different, but everything keeps resetting.

The game is secretly extremely meta and self-aware, much like Undertale.
Expanding on the above WMG, Isaac's world and life is constantly reset and randomized by the player. Maybe the true goal of one or several of the characters (Satan, God, Mom, Isaac, etc.) is to find a "final ending" that will end the loop and allow them to continue with their lives. Maybe we'll even get a True Final Boss along the lines of Sans, whose goal is to get the player to stop playing and resetting everything.

Isaac's mom did hear a voice...but it wasn't God.
The intro narration says, and I quote: "...until the day Isaac's mom heard a voice...from above." Note that the narration ''never'' refers to the voice as God, just as "the voice." It could very well be that Mom just assumed the voice was God. In fact, Afterbirth alludes to this: one of the new loading screens shows the intro's scene where Mom hears the voice for the first time...then it pans up to the attic, where we see The Lost speaking.

Isaac is transgender, and Magdalene is her truest identity.

As many people have pointed out, Ending 14 shows a photo of Isaac's mother and father out in the park with a happy girl wearing pink who has Magdalene's blonde wig; Word of God has confirmed that Isaac has no siblings, so we can only interpret this girl as Isaac. A photo that comes after this in the same ending has an unhappy, bald Isaac wearing green. Isaac also has a nightmare about being presented with the wig, being extremely happy upon putting it on, and then crying when other children laugh at her. It's possible that Isaac has identified as a girl since being very young. Isaac's mother and father were accepting at first because they assumed their "son" was just playing dress-up or going through what they saw as a passing childhood phase, but as Isaac got older, her father became less accepting and thus left — which was what drove her mother off the deep end as she blamed Isaac for driving the father out. Alternatively, both of her parents became less accepting as she got older, and they told her being herself wasn't right, possibly influencing her fear of being teased as in the dream.

It's worth noting that one of the first things Isaac's mother takes from her as an "influence of sin" are her clothes — normally, you think of being nude as linked to sin (e.g. lust), unless there's something "sinful" with the clothes you're wearing. (It should be noted that the Japanese associate nudity with purity, but there is absolutely zero indication that Isaac's family is Asian.) Mom probably caught Isaac in a dress or skirt, perhaps something she sewed from "boy's" clothes she had, so decided the only solution was to take away all of Isaac's clothes. There's also the Mom transformation; dressing up in parents' clothing isn't exactly uncommon among any kids, and it has a lot of significance to trans kids. And the pajamas that give you full health and Soul Hearts — dressing in clothing that makes the character feel like herself heals her. That's really powerful symbolism.

As for Magdalene being Isaac's truest identity: Magdalene has the most starting red health out of any of the characters, which can be interpreted as her having the strongest connection to "Isaac's" body and soul out of any of the characters. Isaac is also wearing the Magdalene wig in the flashback looking happy, and is happy in it again in the dream between floors. The base character doesn't have that kind of connection to any separate character except Azazel, who's more linked to Isaac/Magdalene's fear of developing into a demon than it is to her personal identity.

  • Partially jossed. Mom's full name is "Magdalene", per the Divorce Papers art in Four Souls and Isaac's dad calling her "Maggy" during the Ascent in Repentance, and the Magdalene character in-game likely represents a more empathic version of her.

The sins don't actually represent Isaac's sins, but rather how Isaac *perceives* himself.
Think about it: Isaac is just a kid, can he really be capable of harboring such horrific manifestations of greed, lust, sloth, etc.? No. He's just heard his mother talk about sin, and internalized all that talk to assume — and to fear — that he contains all these horrible sins that he has to battle and kill before they consume him. They're really just the manifestations of that fear, not manifestations of the sins themselves.

??? represents Isaac's mind, rather than his body.
The Lost has three items that it can unlock by defeating ???, Satan, and the Lamb: The Body, the Mind, and the Soul, respectively. If ??? represents Isaac's body and the Lost represents his soul, then it stands to reason that there must be a character who represents his mind as well. But who could it be? Magdalene, who seems to be Isaac's most commonly used "persona"? Azazel, who, like ??? and the Lost, starts with no red hearts? Apollyon, who might represent the Void? None of the above. Isaac's mind is, in fact, ???.

Isaac's body is instead represented by Keeper, as evidenced by the username of Greed's official Character Blog, "iamisaacsbody". Keeper, unlike Azazel, but much like ??? and the Lost, can't collect red hearts at all. He instead collects coins for health, and coins, like the body, have a physical presence, as opposed to Soul Hearts or, in the Lost's case, nothing.

???'s appearance is how Isaac imagines his own dead body: A cartoonish, blue corpse with X's for eyes and nothing but poop as a means of defense. Keeper, on the other hand, is what remains of Isaac's actual body: A colorless, shriveled, and highly unsettling carcass whose organs decayed long ago.

If that's not enough evidence, consider each character's debut. ??? first appeared in the original Flash game, which took place entirely in Isaac's mind. Every level, every cutscene, not once do we see so much as a glimpse of Isaac's real life before the Halloween update and, by extension, Wrath of the Lamb. And even then, defeating ???, the definitive final boss of WotL, yields an ending consisting of photos of Isaac's memories, the deepest part of his mind. Then comes Rebirth, the first appearance of the Lost. Rebirth really piles on the evidence that Isaac is dead, with only his soul remaining. Afterbirth then introduces Keeper, along with a new ending that outright confirms that Isaac is dead, with Mom opening the chest and finding — you guessed it — Isaac's body.

With all this, it can be concluded that Keeper represents the Body, ??? represents the Mind, and the Lost represents the Soul. (Though nobody ever questioned that last part.)

Azazel, in addition to being how Isaac sees himself as a demon, is some kind of Parody Sue-ish character out-universe

Most of the other characters just have one or two visual traits that separate them from the base Isaac (Cain's eyepatch, Judas' fez, Magdalene's hair and bow, etc) or are just Isaac in various states of death (???, Keeper, and the Lost), along with an item or two. Azazel, on the other hand, is a flying red-eyed demon that can shoot blood lasers, has asymmetrical horns, pitch-black hair, and is extremely powerful to boot. Heck, he can even teleport, by means of starting off with a Fool card. It just kind of brings to mind something like this.

So... maybe Azazel is also some kind of character in Isaac's drawings that embodies what he "thinks might be cool?" (If sinful?) No idea about Eden, Lilith, or especially Apollyon, though.

Isaac's parents were not abusers.

As of ending 20, we get a sense of just how severe Isaac's self-loathing is. All the horrible things depicted or implied aren't Isaac's memories; they're what he thinks he deserves.

Isaac is a Child by Rape

WARNING: UNMARKED SPOILERS. YOU HAVE BEEN WARNED.

It has already been stated that Isaac has self-loathing problems. In Ending 20, we see that Isaac has drawn himself as a demon and even calls himself the devil. I believe that this is because his mother was raped, and Isaac is the result. The reason that Isaac's dad left was because he couldn't deal with his wife's issues stemming from the trauma (or he could have a problem with raising a child that wasn't his, or maybe the child IS his...) and divorced the mother of his child. The Scarred Womb is further evidence for this theory. It is torn, ripped to shreds, bleeding in some places. And what else would we fight in there but Isaac himself, in the form of It Lives? The other Womb levels are just your run-of-the-mill womb levels, but even then, they have monsters running around inside of them (up to and including actual literal tumors). And what Horseman of the Apocalypse is fought in the Womb levels? Conquest. Make of that what you will. And in the end, Isaac in effect undoes his own existence. This is because he knows what was done to create him. He wishes he was never born because of all of the pain his biological father caused. Being a child, he believes the blame rests on him. That black shadow at the end of Ending 15 could represent his own sins, real and imagined.

Each final boss represents a mental function, and defeating it symbolizes it breaking down as a consequence of Isaac's gradual brain death.

UNMARKED SPOILERS

  • Mom: Represents Isaac's capacity for rational thought. The whole game, starting right from the intro sequence, is of course a delusion brought on by lack of oxygen, but up to and including the Mom battle, it's at least a logical, self-consistent delusion, if a somewhat fantastical and especially gruesome one. Everything from The Womb onward is bizarre symbolism that makes no concrete sense and doesn't fit in with the plot — at least, not the plot we're presented. Goodbye, logic.
  • Mom's Heart: Represents the last vestiges of Isaac's damaged self-esteem. We know Isaac hates himself and thinks his parents' breakup is all his fault. He hid in the chest because he had to escape his feelings; it was too much for him to live with. When you defeat Mom's Heart, that's where the feelings come back. Even though Isaac has already saved himself from Mom and exacted his revenge against her, he's now going one step too far, infiltrating her unprovoked and hurting her in an intimate way. This isn't heroism. Isaac is no longer the hero of his own invented story — merely the protagonist. Just the way he feels it's been all along, and just the kind of thoughts he tried to lock himself away from. He no longer possesses the faculties to keep them out. Goodbye, peace.
  • It Lives: Represents Isaac's cognitive ability to distinguish himself from anything around him. It Lives is a memory of an important fact: that he was once a part of his mother, and he came from her, and now he's something else. As he kills It Lives, he mentally retreats back into Mom's Heart and becomes one with all he knows again, and begins getting his autobiographical knowledge mixed up with other kinds of knowledge, hence his self-insertion into his understanding of Christianity in either of the following levels. Goodbye, ego.
  • Satan: Represents the limit of Isaac's knowledge of Christianity, and his intense negative self-image. We know Isaac believes he's the Devil. So when he kills the Devil, that can be interpreted as him losing sight of his self-loathing. It's something strong and painful for him, and it's clearly deeply rooted — in quite a literal sense, given how many trap doors he has to jump down to get there. But, like the rest of his mind, it's subject to peeling away as he dies. Goodbye, sadness.
  • The Lamb: Represents repressed anger that underlies Isaac's self-loathing. Deep down, he knows he doesn't deserve any of this, he's just a child, and by way of fate depriving him of a father and deigning that he should blame himself so severely, he has been wronged. He's reminded that he's not the Devil; rather, he's a sacrifice. His reunion with this lost anger is brief, and he has no choice but to let go of it, because with or without him, it's disappearing. He is losing the ability to feel at all. Goodbye, anger.
  • Ultra Greed: Represents Isaac ability to make decisions. With what little feeling he has left, he wonders if he should have picked a different method of death. Maybe if he hung himself, death would have come more quickly and the pain would have been much shorter-lived. Or maybe the ensuing commotion would catch his mother's attention, finally snap her out of her grief, and rush to his aid? No...suicide is a sin. His mother would likely condemn him for such an abominable act. His breath slowing further, he decides to defeat Greed and resign to his fate in this forgotten chest. Goodbye, critical thinking.
  • Isaac: Represents Isaac's identity, and his ability to filter knowledge and observations through his own personal interpretations and perspectives. Before killing Isaac, when Isaac sees something, he sees what it is to him. After killing Isaac, Isaac goes to the Chest, where he sees things exactly as they are, without interpreting them. Appropriately, killing Isaac is the moment where Isaac is truly mentally dead. The extent of his deterioration has sunken beyond "there is no distinction between Isaac and everything else," and landed squarely in "there is no such person as Isaac, there is only a frightened lost child." The Isaac we see in the game from this point forward is little more than a nameless meat husk with feelings. Goodbye, sentience.
  • ???: Represents Isaac's ability to observe the outside world, and peripheral awareness of his circumstances. His identity was so strongly in denial of his impending death that it had to be destroyed for him to be psychologically bare enough to acknowledge he is dying. However, this lasts only until the Blue Baby is defeated, at which point he cannot acknowledge he is dying because there is no sensory input or awareness of past events left to acknowledge. Goodbye, memories.
  • Mega Satan: I got nothin'.
    • Represents Isaac's ability to feel physical pain. Mega Satan is one of the tougher bosses, and the constant barrage of attacks on Isaac could easily represent all the pain he is experiencing while in his death throes, his body screaming at him as he interprets survival instinct as the personification of evil. Defeating Mega Satan ends the pain, leaving Isaac's body completely cold and numb, letting him die in piece. Goodbye, nervous system.
  • Hush: Represents Isaac's self-preservation instinct. By this point, Isaac no longer knows who he is or very clearly remembers anything about his life. He can no longer think coherently, and if he still hates himself, he no longer knows why. But, as even the simplest animal knows when it can't breathe, he knows he's in grave danger. He doesn't even remember what kind of danger he's in or how he got there. All he knows is how it feels, and it feels how Hush looks. But the warning has come too late. He defeats Hush, and loses the ability to feel the need to breathe. Goodbye, basic animal instinct.
  • Delirium: Represents the whole game. After all is said and done, only the dying dream is left. The boy observing the dream is no more. The dream simply plays on unattended, like a scratched-up record in an abandoned parlor. But all must come to an end. Even madness and shapeless delusion slip away eventually, and if nothing is underneath them, then nothing is left. The mindless crying zombie defeats Delirium, the world falls apart, and Isaac is dead. Goodbye, cruel world.

Mom, while abusive, doesn't actually want Isaac dead. Isaac only thinks she does...and also thinks she's justified.

WARNING! UNMARKED SPOILERS!

Everything in the game related to happy memories shows the whole family together: Isaac, Mom, and Dad. However, once Dad leaves, things start getting bad. Mom is obviously distraught and finds two ways to try and cope with the situation: Religion and...lashing out at her son.

The things she does in the intro after hearing the voice of "God"...that's simply unfair punishment. Taking away his toys and clothes, that had no actual religious (or delusional) reason, it was just her punishing her son for misbehaving. However, that punishment was way too harsh for whatever Isaac did, because she was lashing out at him in her distressed mental state.

When it comes to religion, she chose to watch those "Christian broadcasts", which were all the "fire and brimstone" type preachers. Isaac, obviously, also watched those. And that led to him developing a really bad self-image. He thought himself to be the reason his dad left, and with that, the reason why neither him nor his mom are happy anymore. For a young child like Isaac, that was the worst thing he ever did, and maybe — in his mind — the worst thing anyone could ever do. So who do these men on TV say is the ultimate evil? Satan and his demons and followers. God hates them! And Isaac sees himself as one of those demons.

Eventually, he might have stumbled upon the biblical Binding of Isaac. Maybe it was part of one of the TV sermons. Hearing his name and God wanting him dead scared him, so he never actually heard the real ending to that story and became convinced that his mom will eventually kill him on God's behalf, because after all, he's the most evil thing he knows.

The whole game is a mental struggle between his self-loathing and sense of self-preservation. He thinks he deserves to die, but also doesn't want to die. He imagines a fantasy world filled with terrible horrors, in which he fights things representing his corruption: Demons, personifications of The Seven Deadly Sins, harbingers of the Apocalypse, and of course, Satan himself. A part of his mind wants to prove that he's better than he thinks he is. Although it is telling that, to defeat the ultimate evil (Mega Satan), he either needs the key belonging to his dad, or to kill literal angels, servants of God.

In the end, despite confronting his fear of what his mother thinks of him (Mom), his own self-loathing (It Lives, Isaac), the representation of Evil and Sin (Satan, Mega Satan) and even his own suicidal thoughts (???, Hush) and mental illness (Delirium), it's too late. Maybe he did decide that he deserves to die, or maybe by the end, he didn't have the strength to get out of the chest. Either way, he's dead.

Boss symbolism in relation to the game's lore and motifs

WARNING: UNMARKED SPOILERS AHEAD

I'll be going through the symbolism I perceived from the final bosses in the game based off the game's lore, references, motifs and other occasional outside sources.

Mom: After going through the entire plot and all the endings, I'm pretty sure Isaac's mother isn't actually chasing her son down a long, winding, variable basement with a knife on hand, ready to kill him to serve God. But if the game's cutscenes have shown me anything is that while she's not a psychopath, the mother is most likely abusive, at least psychologically. I get that the point is that Isaac sees himself as a literal Antichrist, but that low self-esteem is definitely not something he just gained one day, something caused it, and his mom's actions towards him might have been it (and his father probably wasn't much better).

For starters, her main direct attack is her leg and foot stomping down onto Isaac. Since she's abusive, this is probably what she's done to poor Isaac, trod over him and keep him on the ground, lower than dirt on the bottom of her heels. This also might explain where the game's fascination with poop comes from. We see time and again that Isaac remembers his mother giving him poop as gifts (but then again he also "remembers" being short enough to only hug her leg, so make of that what you will), his health recovery items are two things you give a pet (a dog food bowl and a cat food can) and expired milk, so their health is probably not the best. The expired milk also brings to mind the fact that, after Isaac's father left, the mother really let herself go, which also brings us to her appearance. All that we see is her gross, varicose-ridden leg, her eyes and flab almost pouring out of the room doors, while her voice is distorted and demonic-sounding. Probably because Isaac's so used to her abuse that the mother he once thought was loving and nice is now only a grotesque monster, and her uglier aspects is all he can see.

Mom's Heart/It Lives!: So Isaac perceives his mother as an inhuman monster. Somehow he figures out that, in order to truly "kill" her, he needs to take out her heart... in her womb. Isaac being a kid might have something to do with this, probably didn't get to a big enough grade at school to learn about anatomy and just thinks the heart is "inside the body" to some capacity. He does associate the womb with "being born", at the very least knowing where he came from. As for why he's fighting Mom's Heart, well, she's certainly experiencing a heartache. Her husband left her, for reasons we still don't quite know for sure, and most likely she's taking that frustration out on her child, who sees himself as a demon his mother doesn't love. Fighting his mother's heart is probably his way of interpreting that heartache she feels, that giant, heavy heart who now beats furiously out of all the sorrow she must feel.

And then defeating it enough times reveals It Lives!, which is Isaac as a fetus, as confirmed by Edmund himself. This, I think, is when Isaac's mindset shifts from "blaming yourself for your mother's suffering" (which also explains why most enemies resemble Isaac in some capacity) to truly, and literally, "wishing you were never born". The name is often punctuated with an exclamation mark, like it's a statement. As if it's a surprise that it's living, or that it SHOULDN'T be living. I don't think there's more to it than that, honestly. Isaac at this point wishes he could just flat-out abort himself so he won't cause anyone anymore pain, as he perceives it.

Satan/Mega Satan: Why would Isaac fight Satan despite the fact that he thinks of himself as a demon? I think it's part of the whole theme regarding the observation of corrupted Christianity. Satan's grunts and demonic voice are actually reversed and down-pitched voice clips for Mom, which could hint at an association, not between the Devil and Isaac's mother, but between Satan and her beliefs. If his overly-religious mother was a fan of using the Bible to aid in her abuse in some capacity, Isaac could be filtering the religion and feel so much spite for it that he actually can't see anything past Hell or the Sheol. He associates himself with both concepts so thoroughly that he thinks he's beyond saving. Alternatively, fighting Satan might mean he's trying to defeat the evil inside himself, or at the very least coming to terms with the fact he's "impure", which leads into Mega Satan.

Several items in the game hint that Isaac, at least at some point in his life, had access to classical video games. It dawned on me that someone, I don't remember who, mentioned once that Mega Satan seemed a bit too "videogame-y", so maybe that's exactly where he comes from. Isaac is manifesting Satan as this powerful, hard-to-beat final boss from a videogame, with a name so imposing that it's almost silly.

The Lamb: First there's the better-known explanation for this boss, the fact that he's called the Lamb, which is one of the names used to refer to Jesus Christ in the Bible. If Isaac has been abused by his mother in some form related to religion as stated above, he probably doesn't have the best view about it, to the point where he'd probably see a figure known as a savior as an ugly, decayed demon instead. But there is another theory surrounding the Lamb that caught my attention.

(credit to Youtuber "Millsbuddy", first pinned comment found here)

There is a recurring theme in the game regarding the trinity of the Mind, the Soul and the Body. Three items in the game with these exact same names can be obtained, all of which you unlock by playing as the Lost. And these same items come from what could be said are evil counterparts to different aspects of Isaac:

The Mind is unlocked by beating Satan. The Mind is Isaac himself, since the entire game is his Dying Dream and thus everything is (technically) under his control. Isaac sees himself as impure and unholy, and thus this leads to the Christian interpretation that Satan is controlling him, therefore representing the Mind, ISAAC's mind, being held by evil incarnate.

The Body is unlocked by beating ???/Blue Baby. I'll get into Blue Baby more into detail in a bit, but he IS Isaac's own dead body, a body in the literal sense, so no further explanation needed here.

The Soul is unlocked... by defeating the Lamb. The only character in the game who is a go-to "soul" that gets even the slightest bit of focus is the Lost himself, Isaac's own soul. The Lamb is therefore an evil counterpart to the Lost, as a demon that represents Isaac's soul and what he perceives it to be, something evil and corrupting of Christian beliefs. Why else would it start the battle in Isaac's signature crying pose? It's another monster Isaac sees in the mirror.

Isaac: It's no surprise by now that Isaac thinks he's beyond salvation, and has a very low view of himself. Fighting a literal clone of himself was honestly kind of inevitable. But interestingly, his clone is fought in a cathedral and it gains holy powers and angel wings to use. Since Isaac likes to pit himself as a demon or impure because of his parents' separation, him fighting a holy version of himself probably means he's either given up on salvation or coming to terms with his low self-esteem, actively fighting the part of him that thinks he can be saved. So he defeats this version of himself which, during the battle, goes through phases that indicate a godly awakening or ascension (crying in despair, sees the light, ascends into an angel form), and when it's defeated, it doesn't as much die as it flies off into what might be Heaven. He's accepted he no longer can be saved or doesn't deserve it. The idea of hope leaves him for good.

???/Blue Baby: Isaac's dead body. His view into the future and what he'll become. The Xs for eyes and the blue coloration are both cartoonish signs of death, and Isaac is, at the very least, a young child. It wouldn't be too outlandish to assume that he'd see the final result of his suicide as this lifeless carcass, blue from suffocation and dead for good, with the Xs for eyes to prove it, since it's the best way he can identify a dead body at such a young age. And given that it somewhat copies Isaac's boss form's phases, Isaac is coming to terms with the fact he's going to die in the chest the same way he comes to terms he's beyond salvation. He's seen his future once after fighting It Lives! in the womb, now he's accepting it.

Hush: Back to the theme of an Evil Counterpart, there's a parallel to be traced between the two accessible routes after the Womb. The Sheol and the Dark Room are the "evil" route, while the Cathedral and the Chest are the "good" route. But the only other distinct final boss known for a lot of HP and constant attacking is Mega Satan, which is fought on both extremes of each route, almost like it's a level of his own. That's what the Hush is, the parallel to Mega Satan, as a final boss with even MORE HP and even more relentless attacking, fought in a level entirely dedicated to him (albeit actually considered a separate level and larger than just one room). Hush itself is essentially a more powerful Blue Baby to Mega Satan's more powerful form of Satan, to the point where it even starts the battle as a repeat of the Blue Baby fight before becoming its true form. And yes indeed, a blue creature that looks like a face smothered under a fleshy membrane, all of which represents suffocation, Isaac's chosen method of death.

I also realized that one could maybe define this relation as an extreme to that trinity of the Mind, Body and Soul. Except here, with Hush being the extreme of the Body (since it's basically a MUCH stronger repeat of Blue Baby), Mega Satan becomes the extreme of the Soul, representing Isaac's perceived corruption and inner evil. This same page has a theory where Isaac sees himself as a demon to the point of embodying every evil aspect described in the Bible, down to the Harbingers and the Seven Deadly Sins, and having to kill Angels only to have them fall, all of which appear during the Mega Satan fight. So that would leave the extreme of the Mind, which leads to...

Delirium: You can't be more extreme than a boss which becomes all the other bosses (sans Ultra Greed). Delirium is definitely the extreme of the Mind, or rather, the death of the mind. The Void is an area made up of all the previous areas, and Delirium is a boss made up of all the previous bosses. Isaac's mind is shutting down, his imaginary world is crumbling apart. The Void is a mishmash, glitchy and imperfect, with rooms changing layout when you leave and re-enter and even as you go from one door to another. The entire area gives this eerie feeling of instability, like the game itself is being slowly deleted and unable to process the data that's left.

When you look at this monster, you don't think this thing is at all "stable". Its face, which is the creature's entire self, is melting. Every time it shifts into another boss form, that boss is also shown to be melting, and the glitching effects might still occur as the boss takes more and more damage, which will cause the arena to change. It becomes faster and more aggressive as it dies, because Isaac himself is probably at his last breaths, increasing the pace because his lungs are losing oxygen, so his body instinctively tries breathing faster to get any molecule it can to stay alive. When Delirium does finally die, the arena defaults to the layout of the Chest, because it's the closest to "reality" Isaac can get, the awareness of his tight surroundings.

When Delirium dies, so does Isaac.

  • I really would like to see an update for the Repentance Bosses now. This sounds like an incredible theory!

Delirium will be made a playable character in the Repentance expansion.
So far, he has two items based on him: Delirious (which summons a charmed Delirium to fight for you), and Lil Delirium (an item added in the first Booster Pack which summons a familiar version of Delirium). It would make sense that Delirium's gimmick as a playable character would be that he can transform into different playable characters during a playthrough under certain circumstances.
  • Not quite confirmed, but very close. Tainted Eden is essentially a playable Delirium in all but name. While they don't transform into other playable characters as described here, their gimmick basically turns them into a new character every time they take damage.

One of Isaac's parents was a doctor.
Could explain the presence of multiple items in the basement, such as PHD, IV Bag, Stem Cells, and all of the syringes and pills.

Isaac's did NOT commit suicide in ending 20
think about it, hes a skeleton covered in cob webs when the box has opened, implying a LOT of time has passed, if he killed himself and his mother was actually looking for him, surely she would have searched his room thoroughly, or even if shes not observant or wanted to avoid his room do to the memory's, she would have HAD to have noticed the smell once he started rotting, unless she was deliberately not trying to find him, that or the box being opened at the end is not the toy box he suffocated in, but the casket he was buried in, which begs even further questions
  • Almost. You were Right for the Wrong Reasons. Isaac did commit suicide by suffocating himself in a chest, but it was just a bedtime story he created with his father.
    • Jossed again. Isaac indeed is dead by the time Ending 20 rolls around.

The ending of Repentance is the aftermath of Isaac's father divorcing his wife and winning Isaac in a custody battle.

The voice at the end is not that of Isaac's father, but God Himself
.
  • With Edmund confirming that Isaac is still dead at the end of Repentance, my mind tried to make sense of the last ending. At first, I thought it was Isaac finally being at peace in his last moments, but then how would he have known that his mother would be mourning him? Then it hit me: this is God talking to Isaac. He probably has a similar voice to Isaac's father because He wanted to sound familiar to the young boy and since many refer to God as a father, that's what Isaac does too.

Bumbino is a different side of Isaac's father
  • Bumbo, both in this game and in Legend of Bumbo is shown as a sympathetic character as well as being a representation of Isaac's father himself in the Bumbo game. So, why is a giant version of him a possible boss? It represents Isaac's father when he got drunk. The usually sympathetic character that Isaac loves to see suddenly turns into a violent being that breaks stuff around him, lashes out and can clumsily crash into a wall. Shooting Butt Bombs could be him still trying (and failing) to amuse Isaac and the possibility of him leaving if he collects 10 coins during the fight could represent that if his dad found money in his drunken state, he would just leave to get more drunk.
    • Alternatively: Bumbino is the original creation of Isaac, representing his dad as an angry, lashing bum who only cared about getting money. Similarily to how Isaac's mom found the drawing of Mother in an ending, his dad found the drawing of "Bumbino". Unlike Isaac's mother, dad took the idea of "This is how you see me? As a monster?" in the opposite way and decided to stop drinking so his son wouldn't see him as a monster anymore, hence why Dad's Coin (which is shown to be an Alcoholic Anonymous token) is so important to Bumbo, the funny, sympathetic version of Bumbino, which Isaac later created to show how he now sees his dad.

Isaac's father died at some point after leaving Maggie, and in the final ending he reunites with Isaac in Heaven.

The arcades represent Isaac's father's gambling addiction.

In Repentance's final ending, Isaac "saw nothing" because he went back in time to before he was born
If you look closely, the events in the final cutscene fit in reverse chronological order: he dies from suffocating in the chest, his father leaves, his father steals money (resulting in his leaving)... at the very end, he sees his own birth. Furthermore, the Ascent itself involves going through all of the explored floors in reverse order, ending at where he was before he even imagined himself in the Basement. So, what is his life like before his birth? Nothing.

Lilith is another representation of Mom
I saw this theory on Reddit, actually, and it makes a lot of sense. Basically, Lilith is the demonic counterpart of Magdalene, who is Isaac's desire to be like his mother. In the context of the game, Lilith's starting Incubus would thus represent Isaac himself, with Lilith being his mom who blindly leads him along. This Incubus would have the same context as Azazel, being Isaac seeing himself as full of sin.

Greed as a whole represents Isaac's father
The Beast ending and the Ascent highlight an important thing in the backstory: Isaac's father stole money from his mother while she wasn't looking. This is most likely the source of why Greed is so ubiquitous throughout the game, culminating in Ultra Greed. Additionally, two specific Greed Mode unlocks are: Dad's Lost Coin, an Alcoholics Anonymous token, and Dad's Ring, which is Dad's marriage ring. These two are unlocked with the Lost and the Forgotten, further highlighting the significance.

The Tainted characters are the original, primary versions of the normal characters
Let's start with how you unlock the tainteds. To ascend back to Home, Isaac needs to find his dad's note. Since he relives the argument that lead to his parents divorcing, it's safe to assume the note was his dad's goodbye note to him that caused moments Isaac repressed to come back. The Mother ending shows us that the mom locked her child in a closet as punishment. Where do we find Tainted characters? Lying in a closet. From the same thought train we can deduce that the Red Key is the key mom used to lock the closet. The achievements you get from unlocking these characters are all condescending in nature: 'The Deceiver','The Savage','The Capricious' etc. These all could have been things Isaac's mom called him when she was angry. In the same ending, we see Satan's figure fading into view while Isaac sobs in the closet. This could represent Isaac embodying his wrongdoings as characters. Isaac gets caught lying? While in the closet, he thinks up of Judas, a deceptive backstabber. Isaac poops himself? That's where ???, someone with nothing but his own feces, comes from. Isaac is caught stealing? That's how the scoundrel known as Cain is born. Over time, these alter egos mellowed down due to Isaac getting used to the abuse, but finding an old note and refreshing his memory, the roots of the playable roster came back as Tainted characters. Why tainted? They came from taints Isaac's mom perceived in her child.

The game is Issac's journey through Purgatory.
Or as I like to call it, Issac's Ladder. Even before the confirmation that the game was Issac's Dying Dream, I assumed he'd died and he was fighting the sundry monsters, lost souls (including several of his stillborn/dead siblings), and demons in Hell, just judging by all the blood, shit, bugs, etc lying around. There's even a supporting theory that the Golden Ending is Issac telling God his life story. Each "new character" being a part of Issac's mind/soul/whatever represents something he needed to deal with before he was ready to go to Heaven.

The Alt Floors from Repentance are based on Hell Circles from Dante's Inferno.

Here is my interpretation: Alt floors could be a reference to Dante's Inferno, with darkness and evil increasing the more Isaac descends into the depths of Hell, all goes without mentioning that the depth of each floor's location corresponds to the depth of the circles' location in the Divine Comedy. Downpour is an eternal storm, so is the Lust circle. Dross has sinners drenched in water full of excrements, just like in the Gluttony circle. The Mines are filled with lava, in the violents' circle, sinners are left in boiling blood, which, in several depictions, is represented as lava. Ashpit is an endless desert where fire rains, like in the sodomites' circle, the Phrygian scale of Absentia, the floor's theme music, really conveys the idea of a desert. Mausoleum is filled with sorcerers, in the Malebolge, sorcerers are punished among the various sinners located there. Gehenna is a place of heresy whose walls are crimson, much like the crimson graves of the heretics' circle. Corpse represents the betrayal of family, which is self-explanatory, given that it's Isaac's mom's dead body... Because he killed her to get there, also the ending you obtain for killing Mother shows Mom feeling betrayed by Isaac when he showed her how he truly felt about her.

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