Zacharie is the guardian of Zone 0.
Both the inside and outside areas play a version of "Empty Warehouse." Considering that Zacharie is a merchant, him owning a warehouse isn't out of the question. As for why it would be empty, Zacharie seems to carry all, if not most, of his stock on him because of his occupation of a video game merchant.
  • The reason why Zacharie doesn't show up in Zone 0 for most of the game is because he's busy doing business in the other zones and the warehouse is empty, anyway.
  • Zone 0 is one of the last zones standing after the other guardians have fallen.
  • Both Zacharie and Judge appear to frequent Zone 0, and the two appear to friends, or, at least, Zacharie recognizes Judge enough to notice when he leaves to mourn the death of his brother in the remains of Zone 2.
  • Not to mention how him and Sugar know each other as well, at least enough for him to mourn her death.
  • Jossed. According to Word of God The Judge is the guardian of Zone 0.
    • Furthermore, remember what the Judge does at the beginning: He gives you a card that will send you to the first area. Only zone guardians have these cards.

The Batter is a deity deciding that creation is corrupt and deciding to end it all.
Adding to the 'judgement day' interpretation of the game is the fact that all of the zone bosses (except for Sugar and the Queen) are named after descendants of Noah.
  • Alternatively, the Batter is just the emissary of this deity. You, the player, are the angel guiding his steps, and the deity itself is the one who "assigns" you to the Batter. Mortis Ghost, maybe?

It was Japhet's madness that made Dedan the jerk he is in-game.
The room seems to imply the three were good friends at the start, and most of Dedan's cruelty is towards the Elsens. Perhaps seeing his friend try his best to please them, only for the Elsens to reject them due to their own paranoia, and watching him descend into madness due to his best efforts getting (unintentionally) thrown back on his face, embittered him against them. Perhaps he now thinks trying to be nice to the unappreciative morons that reduced one of his only friends to a violent madbird isn't something he's gonna do, and takes his rage out on his employees.

The game takes place within the Batter's mind as he achieves mental purity.
He is freeing himself of all internal stress (Zone 1), worries (Zone 2), desires (Zone 3), and dependence (The Room).

When all of the zones have been purified, you can hear the Elsens' cries for help.
When wandering the purified zones (1, 2, and 3), the piece heard in the background is called "Not Safe." The piece consists of whispering, desperate thumping and cries for help. During the game, Enoch mentions that without him, the citizens of the zone will fall into an eternal nothingness. It could be speculated that these cries for help are the Elsens lost in this nothingness and are desperate to escape, instead of them just disappearing.

The plot of the game is based around Batter's battle with and descent into possible schizophrenia.
  • Delusion (most common schizophrenia symptom): Batter is dressed like a baseball player with the idea that he is meant to purify the world. His 'sacred duty' is the reason why he killed his wife and child.
  • Hallucination: The existence of the surrealistic Zones and The Room, including how he sees The Queen (his wife), Hugo (his child), and The Three Guardians (the stressors/burdens he carries with him), including hearing voices once 'Not Safe' begins all suggest hallucinations. Perhaps this is the reason for the note at the beginning that says "Keep your volume on to get the full experience".
  • Other symptoms Batter has, related to schizophrenia, are as follows: lack of emotion (obvious visual representation) and social withdrawal (in terms of his family, particularly his son, as read in the notes)
  • The names for Judge's competences (Aneurysm/Sclerosis) are based on trauma to the brain and could possibly be associated with schizophrenia; there is obviously a connection with this to Batter's condition. Judge COULD be the personification of his disease.

Zacharie is Omnipotent
This is why he's one of the only characters you don't kill, one of the few that break the fourth wall, and the only one besides Batter and The Judge that's able to appear in Zone 0. It also explains how he's made out to be so important but outside of selling you goods and providing some exposition he really doesn't do much in game.

The "off" switch is for Hugo's life support machine.
The entire game is a coma-dream of Hugo's, and represents his father trying to get through to him to tell him he has to die. He hides behind his childhood friends and his mother, and fears his father because he doesn't want to die, but in the end, the switch is still turned off.
  • Alternatively, the whole thing is Hugo's coma dream and the zones dying off are parts of his brain gradually shutting down. In the Batter ending, Hugo dies, while in the Judge ending he survives but is doomed to forever be a "vegetable" in a coma, since his entire mind has shut down, including what made him aware of his own existance.
  • Another alternative; each zone is The Batter overcoming an obstacle (local and/or national laws, the mother's agreement/consent, the doctor's agreement to do so, etc.) in being able to turn the life support off so that he can let his son die in peace. In the Batter's ending, he succeeds. In the Judge's ending, he fails.

Sugar killed everyone in Zone 0 beforehand.
Knowing how sugar is made, it's somewhat suspicious how she manages to have so much in her room. Perhaps she was already mad and needed the sugar to calm herself, then had herself sealed in the basement by Zacharie after realizing what she just did.

The Judge is the Guardian of the "off" switch.
And he has his title because he can judge whether or not the world continues to exist, which is why whether he lives or dies determines the ending. He was snapped out of his Despair Event Horizon by the Batter approaching the switch because he has a link to it, and he didn't oppose the Batter purifying other zones because there's a chance for things to be rebuilt as long as the switch remains "on" (chalk it up to the...unique morality of being both a cat and Guardian).

The Batter is a "failed" Guardian of sorts.
Specifically, the "Death" to the Queen's "Life". The Queen is stated to have recreated the world, but may not have the capacity to destroy it, which is why she created the Spectres to correct things for her. Conversely, the Batter can only destroy things, which is why he spends the game purifying the world instead. In the battle against the Queen, she mentions asking the Batter to return to where he came from, possibly meaning another Zone, possibly the Nothingness.
  • On a less serious note, all the Guardians have a quirk to them. Dedan's is pedalos, Japhet's is books, Enoch's is cake. The Batter's would probably be roller coasters.

Zacharie and Sucre are Hugo’s real parents.
But they were separated from him when he was just a baby, so he made the Queen and The Batter to replace them. Now that Hugo is a small child, he doesn’t remember his real Mama and Papa, which is why he says in his diary/notes things that Zacharie is just his friend. Furthermore, Enoch is Sucre’s father, making him Hugo’s grandfather.

Hugo used psychic powers to revive his parents, and the Batter Came Back Wrong.
After the End, exposure to fallout (it's been mentioned that the game's elements are all rumored to cause cancer, so nuclear involvement is likely) mutated his mother and father. Hugo was born sickly, but with powerful psychic abilities - as he was too young to control them, his mother channeled them to recreate the world. Of course, everything turned out more than a little strange as he knew nothing about the previous world or concepts like death, but the survivors figured it was better than nothing and set out to improve it. However, at some point, Hugo's parents succumbed to radiation sickness and died. Hugo brought them back, but in warped forms because of how he remembered them (the Queen's tentacles and "Bad Batter" were how they looked because of mutations). His relationship with his father further colored things; he's a sociopath because he neglected Hugo, who couldn't conceive of any positive traits in him. The final nail in the coffin was that the resurrection process seriously messed with the Batter's brain, which led him to try and wipe everything out and start anew.

The Batter's form changes depending on who's viewing him.
This is confirmed with Sugar and the player alongside the Judge, but this could extend to other characters as well. Early on, the Judge mentions that the Batter has no "physical order", whatever that means. And while Japhet sees him as human, Dedan views him as one of the Spectres, and it's unknown what Enoch thinks of him. Perhaps only people who see the Batter as hostile can see his "bad" form.
  • Perhaps this is why the Elsen are so easily fooled by The Batter wearing a necktie - they actually see him as resembling them, at least until he starts fighting the spectres.

Going off of the above, so does The Queen's.
At one point, Dedan exclaims "By the queen's thousand faces!" despite the fact that The Queen hasn't a single face at all. Seems like just an expression, but we know that Dedan seems to respects the Queen a lot, and thus might view her as a powerful, eldritch being of some sort. Also, The Queen is somewhat presented as an opposite/equal to The Batter, what with having her own add-ons and such.

Going off of both of the above, The Queen is the sun that Enoch refers to.
Enoch mentions that the guardians draw off of the infinite power of the sun, even though OFF does not appear to have a sun, nor a day or night in the first place. Recall that in The Room, Hugo's mom was represented in his drawing as a sun, and The Queen is supposed to replace his mom. Enoch has little respect for The Queen, since he immediately suspects you of being sent by her to stop him, so it's possible he views her as little more than an inanimate object, albeit a powerful one of which to draw his energy.

The secretaries are the lost souls of the elsens left in the zones when they are purified.
The secretaries are described as demonic humanoid spirits. Maybe they're not really demonic but angry and seeking revenge on the batter for ending their lives?

The Batter is/was an Elsen himself.
There are similarities between the Batter and an Elsen (one being appearance). It could be possible the Batter didn't want to comform to what the Elsen's way of life was (nothing but work). So, he donned a baseball cap, decided the Zone Guardians had to be destroyed, and became the Batter. The Batter doesn't make the noise that the Elsens do, because he doesn't want to have anything to do with them in that aspect. He keeps calm and collected (seemingly uncaring) in situations, so as not to get too stressed. What happens if you side with The Judge? He finally becomes stressed, and turns into the creature you see (his burnt form).

There is a power higher than the Puppeteer.
During the beginning introduction it's said that "You have been assigned to a being called The Batter. The Batter has an important mission. Be sure that it's completed. We will let you out in Zone 0. Good luck." This implies that even though the Puppeteer is thought to be God, something is giving the orders.
  • Perhaps monkeys from beyond the stars?

If the Secretaries Divide By Zero attack was used anywhere else, it would cause a Reality-Breaking Paradox...
...but in the Purified Zones, reality is already broken.

The Spectres are the angry souls of the Elsen.
They are getting their revenge for being processed into sugar... And the Batter turning Elsens into Burnts and then slaying them sure isn't helping matters.

Zacharie will or has gone turbo before.

The Batter is performing the ultimate Mercy Killing.
The Batter knows that the world he lives in is a Crapsack World, and wants to destroy it so nobody has to live there anymore.

The Batter is an adrenaline junkie.

The entire game of OFF is an alternate universe sequel to Earthbound
After defeating the ultimate evil, Ness was extremely traumatized. His innocence was lost, and the boy's smile died with it.

Ness grew up to be stoic, and chose to solemnly DESPISE everything corrupt on planet earth. He believed any and ALL evil in the world must be wiped out completely. Never again, did he want something as putrid as Giygas to pervade his home. In the event of a world shattering cataclysm, however, he vowed that he would take on the responsibility of being the world's savior and purifying the world with his PSI powers.

Although Ness was perpetually solemn and viewed the majority of mortal existence as disgusting, there were a few things in life that made him genuinely happy. While his childhood friends eventually became nigh irreversibly distant, Paula was only a town away. She was one of the few things in his world that remained pure, the only friend who understood him. And of course, Ness never forgot his love of baseball.

Paula and Ness followed one another into adulthood, and eventually got married. The day their little boy was born was supposed to be a happy one...

...Until the end of the world happened, via a nuclear fallout. A really, REALLY big one.

Ness' world previously had its fair share of sentinent animals and creatures, but that was drastically reduced. And there were even fewer humans left. Most of those that were were mutated – including Ness and Paula.

Paula had gained enough prestige as a psychic prophetess of sorts, and was unanimously selected by the remaining populous to be Queen. Likewise, Ness was widely respected as the Chosen One, and chosen to be king.

After a couple years, Hugo grew more and more ill. Yet, he was showing signs of PSI/PK at an alarmingly early age. Ness was unable to aid, as he had lost much of his PSI/PK abilities in the mutation; Paula (now known as the Queen) managed to keep her powers, and even changed them a bit.

Ness could never relearn PSI Heal, which is why he didn't revive any of the world's populous, or heal the remaining populous of their mutations and infirmities. He felt useless to the world, and to his family.

The Queen did her best to care for her sickly child, and help him channel his powers through her own, but all they could do to keep him under control was imprison him.

Ness, on the other hand, chose to depart for a few years, for various reasons. The idea of his only son being forced to live that way was unbearable to watch, he wanted to know if anyone else in the world had survived, and he wanted to find a way to fix the world. Maybe he could even regain his powers. Although much had happened, Ness still remembered his vow to help the world if a global catastrophe ever happened.

After wandering for years in vain, he gets further and further out of touch with the last remnants of his humanity. No longer did Ness remember the love of his family – only that they existed. He felt little to nothing for them, as his mind couldn't supply the will to make such connections. Eventually, the world sinks into more hopeless ruin, and Ness is consumed by one idea: Purify the world... no matter the cost.

Possibly in a last ditch effort by his subconscious to retain his humanity, he recalled a profound love for baseball. Ness rechristened himself as the Batter. Soon, he met up with the Judge.

The sheer amount of concentrated will behind the Batter's ideology was so strong, that it was enough to make his powers return gradually. On his journey, he had been enlightened concerning some matters, such as the nature of Players and Puppeteers, and the role they played in controlling his world. So, he struck a deal with the Player/Puppeteer. By the power of hypnosis, mind control, manipulation of will — whatever you wish to call it – we agreed to help him with his unholy crusade. We had to know how it would all end, didn't we?

Press start.
(Hey, you knew it was coming. Ness often uses baseball bats to attack, and regularly wears baseball caps. Paula seems respected enough in the Earthbound universe to be promoted to queenly status after a nuclear fallout wipes out the rest of humanity. It would explain why Hugo was born with psychic powers, anyway. Plus, Earthbound seems to know it's a video game, as evidenced by how it asks for the Player's name and asks the player for help in the final battle. Kind of makes a chilling amount of sense, when you think about it.)

In the minor 'baseball game' metaphor, The Judge is the ball.
The game begins with The Batter hitting The Judge with his bat, in the tutorial battle. At the end of the game, when The Batter has purified the zones/bases and returned to his home/home plate, he hits The Judge once again.

"Rubber" is actually an alloy of metal and plastic.
Assuming that the world is made of only the four or five elements, that leaves some questions. For instance, we are told that the fences in the residential area of Zone 2 are made of "soft, harmless rubber", which is not mentioned in Zone 1 at all. So where does rubber come from, and why is it not an element? Perhaps because it is two (or more) elements. It can't be just one, because then it would be just that element, not rubber. Smoke is out of the question, because you can't really make something solid out of that. Meat wouldn't be too feasible either, because it probably has an expiry date. And sugar? No one would waste something so precious on things like fences. So the only things left to consider are metal and plastic. Which makes sense, considering metal is solid enough and plastic would be soft enough for a "soft, harmless" fence. Plastic + metal = fence, Q.E.D.

OFF as a whole is about eugenics.
I don't recall where it was said, but Mortis Ghost once said eugenics as a whole inspired the idea behind OFF, and it shows. Consider the player - you - to be a "purist". And The Batter is a tool for which you can carry it out. This is reflected in the gameplay - the first Burnt Elsen you find isn't even really evil, just stressed out. Can't perform under pressure? Well, looks like someone's getting the boot - or, dare I say, the bat. And from a Doylist view, it's not hard to see how Cloud Cuckoolander Mortis Ghost could have dealt with that before.

The game is Hugo's dream, but not his dying one. Instead, it's his nightmare about his dad leaving him.
And to give a starting point: Zacherie is actually an attendant to Hugo, and so goes out of his way to tell him stories and help him through while he gets taken care of for his illness. This is why everybody knows Zacherie and why he's so important, but also so genera savvy. This is always why he's slightly callous about the whole thing in the dream, because he has seen sick children pass away, and so can probably come off as jerkish even if he really does care. The whole story began with Zach letting Hugo choose his own characters in a story, and instead let Hugo decide what was going on. You know, and interactive storytelling experience.

Those who have seen the ending know about the off switch and the space monkeys. Well, it's actually a nightmare Hugo is having. Each major character is based off of people Hugo knows in real life. Dedan is based off of his father's friend from work. This is why he's seen as crass and crude, but in the room he can be seen speaking in a friendly manner when addressing Hugo/The batter directly. His father probably invited Dedan over from work, and Hugo heard some of his crude language. Also Hugo's father probably works in the farming business, raising cattle, which is where he got some of the strange ideas for elements. It is presumably because of his father's more honest nature that Hugo is no longer allowed to see him, because his father probably told him he was at risk of dying.

the bird and the two cats are actually animals he liked to play with. Given that the bird is very indistinct before Valerie is killed by him, it was probably a common bird that Hugo gave a personality to. the whole of world 2 is full of even more neurotic than usual elsens, because people probably always freaked out when they saw him playing with strays and trying to pet wild birds. Given that the bird had no personality to speak of, Hugo believed Beauty Equals Goodness and that the bird was the kindest and most giving of the three. The Face-Heel Turn would most likely be Hugo's fear that the doctors, I.E. the ones who are letting him live, might grow tired of his constant illness and one day wish to stop helping him.

The final guardian was the boss of his mother. He's very kind when speaking, and although he can be blunt, he always explains himself and makes sure he's understood, but otherwise very nice. He was most likely always aware of little Hugo when he was around and tried not to confuse him with adult business, unlike Dedan. This is why he's the kindest of the 3 and the only one who didn't go mad. Hugo doesn't know what job his mother works, so he doesn't associate anything with the boss aside from a nice man. Instead he sees his job as the scary thing. Sugar, I.e addictions and cravings that people buy.

His mother is the queen, who's always busy in order to afford Hugo's treatments. The batter is his dad, who most likely is represented as a stoic version of the bad guy from the comic because he talked more freely about death around Hugo. The argument near the end of the game is something he overheard his parents yelling about. The "you haven't done anything" and "you forgot who the party was for" was his father telling his mother that she was working so much she never even got to see him anymore, despite paying for him to live. She snaps back by telling him he's frightening and saddening Hugo about the very real possibility of death.

The ending of the game was if he feels his old life has gone forever of if he can still keep a part of it. Being a child, Hugo doesn't understand it, but Zacherie does. the official ending is that everything is in the past, and Hugo is no longer living the way he used to be, while the Judge ending is him holding on to 3 people who are still there: Pablo (the stray cat), Zach (his attendant), and a lone elsen (The people at the hospital are still there, even if he doesn't see them as much.) As Hugo doesn't understand the metaphor, Zach instead tells him a new story the next day. a story about space monkeys fighting flying brains, building on the cleared out remains of his old story.

The whispers Not Safe are the Add-Ons reassuring the Batter that his actions were correct.
One of the lines seems to be 'It was good that you killed them'.

The Elsen were meant to be the new world's humans.
The guardians designed them to be just like the men that populated the world before it ended. Unfortunately, the human mind is not prepared for Utopia; fear and danger are an integral part of the psychology that the guardians would have used as the blueprint for humanity.

Without anything to be afraid of, the Elsen had the choice to reject or embrace their genetic disposition towards fear. To preserve their sanity, they embraced fear. Every shadow is a specter, every sound is a slasher, and nothing is safe. And all in the name of being just like humans.

The sequel will be named OFF 2 The Stars.
Warning: Serious spoilers for the Golden Ending.

So, after the Space Apes take over the purified world, we skip ahead a few years. Every zone has now been replaced with a giant robot factory, churning out more and more fighter drones every day to combat the flying brains.

The Player takes control of a random drone, wresting it away from its mission on the day of a decisive battle. The robot armies fall, and the flying brains invade. After successfully hiding from the invading warships, you are left to fight through a roboticized version of the first game to find and defeat the flying brains and restore the Space Apes to glory.
  • Jossed. Mortis Ghost has confirmed he will not be making a sequel.

Dedan chose to have metal form in cows out of spite.
Within the Room, Dedan mentions he's in pain from a cow bite. Assuming that the events in the Room are before the Batter's arrival in Zone 1, it looks like Dedan made his Zone's industry around slicing cows in half just to get revenge on the species. He's got the power to form his Zone to his whims, so why else would he make the decision?

The Batter is the Guardian of the Nothingness.
Before you run from him, Enoch states that the Elsen will be 'forever lost to the nothingness' if he disappears, implying that the nothingness is sort of a place for life after death. Maybe the Queen assigned the Batter to guard this space where the dead go, and the game starts because the Batter's wards, the spectres, escaped; he wasn't used to the way the overworld was, and its weirdness quickly drove him nutso while he was trying to rope all the spirits in.

The Batter is the Queen's eldest son.
While playing the final parts of the game, it seems common thought that Hugo helped the guardians and wrote to his mother, but Hugo is still at least under 5, and in his time the guardians are already not as jovial as they once were.The queen hardly seems to care about anything, so I don't take this as out of her league, especially with her tendency to neglect Hugo, which seems evidence of wanting to forget him despite loving him. The batter on the other hand, is obviously able to do these things and has been able to for a long time before the game, probably back to when the guardians WERE nice. He looks smaller than most of the enemies in game, the queen and guardians included, but when you walk around in the final parts of the game, you play as the Batter, not Hugo, and here he looks even shorter, in comparison to the world and Dedan alike, who when you first fight the Batter is near shoulder height to. Considering most of the other creatures of power in OFF are generally rather tall, and the Batter is always a little shorter than most of them, it would seem he's still young, or at least not fully grown, while the queen is tall and adult as ever. Furthermore, in the Room's notes, it states that Zacharie and Sugar are the writers friends, and while that could easily be true for Hugo, the Batter seems much more likely a candidate considering the age differences. If any of the other in game characters knew the queen was the Batters mother, it could explain certain hostilities or uncare for the queen, although as the Judge decides in the end none of it is excuse for murder. It could also explain why the Batter starts out in the Nothingness, instead of with Eloha and Hugo-she could have sent the Batter away, to prevent the truth from continuing to spread. And the queens comment of, "Look...He has your eyes. They are full of fear.", with the common thought that the Batter has no eyes or at least very different ones from Hugo, this would imply Hugo's creation was less than consensual, or at the very least that she's used to seeing the Batter terrified, and finds he and Hugo to have similar scared faces. Soz if this seems a little all over the place, that I don' have any explanation for.

Zacharie is Hugo's true father.
During Zone 3, Zacharie notices the music box Batter found, and asks for it, saying it would mean a dear lot for him to have it. As we find out later, the music box plays Hugo's theme. Why Zacharie wants something reminiscent of Hugo isn't explained, but we have several hints. First, Zacharie, Hugo and Sugar are all confirmed to be the only humans in the game. Everyone else is a construct. Second, Zacharie follows Batter around everywhere, with Batter (supposedly) being Hugo's father, despite him being a creation of Hugo. Third, during the final zone, there's a paper (one of the calendar pieces I think?) that states Zacharie to be evil and to not listen to him. Given that the final zone is supposed to reflect Hugo, that seems to be his own feelings toward Zacharie. Hugo, too, states to hate his father for his negligence. So going by this, it's not hard to see Zacharie as Hugo's father.

Hold on to your pants, this one's a doozy
The Batter is literally a holy man on a mission to purify the world, created by Hugo. The Judge is literally a cat who is also the Guardian of Zone 0, who teaches the Batter how to fight and guides him on his quest. Dedan is literally a man with a body made of steel, a hard taskmaster, and the Guardian of Zone 1. Zone 1 is literally a living and working area for the people called Elsen, where the four elements are processed and sent where they are needed in the world. Japhet is literally a phoenix who was eaten by a cat, who he then proceeded to possess, as well as being the Guardian of Zone 2. Zone 2 is literally a living area for the Elsen, created by Japhet to make them happy. Enoch is literally a giant man who promised Hugo he would make him sweets, and so set up his Zone, Zone 3, to create sugar for said sweets. Zone 3 is literally an industrial area that produces sugar. Vader Eloha is literally the Queen of whatever world OFF takes place in, as well as Hugo's caretaker, as well as being created by him. Hugo is literally a little boy who seems to be sickly, who is the Guardian of the Room, and the creator of the Batter and Vader Eloha.

There are no metaphors. What happens in the game is literally what happens.

Sugar isn't actually made from corpses
, it's just extracted from it.

It's never really explicitly stated that sugar is directly made from corpses. It's entirely possible that there is simply a very limited amount of sugar in existence, and it can't be produced conventionally fast enough to properly replenish the supply. Likewise, the fact that sugar can be extracted from dead bodies by burning them was likely discovered accidently, considering that the spectres are implied to have begun showing up very suddenly, and its entirely possible that some of them just had inexplicable fire attacks. Enoch probably just decided to run with it, and it likely wasn't his original plan, especially considering the events of The Room, where most of the guardians are revealed to have actually been rather kindhearted and friendly, and likely driven to the states of madness and rage you found them in by the sheer logistics of managing the world.

Zacharie was responsible for the first apocalypse, and is aiding the Batter in finishing the job.
In one of the books in the library, there's a story about a masked man who killed the toad king. The batter killing the queen (and, after her, Hugo), are the last obstacles to the switch. Corollary, even though Zacharie is stated to be friends with The Judge and Valerie, and obviously close to Sugar, he doesn't only not do anything against the Batter who murdered Valerie and Sugar, but also aids him in quest to destroy everything.

Zacharie is clinically depressed.
Mortis Ghost referred to him as a hero, he was the owener of the amusement park in Zone 2, but during the game, he does not act against the person who killed two of his close friends but sell him equipment so that he can better continue on his quest to murder everything, metaphorically handing the Batter the noose to hang him with.

The story is not about the Batter. It's about Zacharie.
Going from the theory that Zacharie and Sugar are Hugo's parents, and that the Batter and the Queen are just stand-ins, created by Hugo. (And that the Judge and Zacharie are in reality two sides of the same coin)
Hugo is sick, and Sugar either couldn't deal with this, or Hugo's sickness started after Sugar's problems, but Sugar is addicted to her namesake (maybe her name isn't even Sugar, but she has gone so far it might as well be). and is absent, she can't take care of Hugo.
Zacharie, faced with his son's illness and his wife's addiction, Zacharie takes more and more risks to support both of them.
The Batter (and, by extension, the player), are a symptom of Zacharie's attempts to salvage what is left is his family actually destroying everything - The Judge believes them to be phantoms at first, but welcomes them - no price is too high. The purification of the first zone symbolizes Zacharie's loss of grip on reality, as the first zone produces the things that make up the world.
The purification of the second zone symbolizes Zacharie losing his job (director of an amusement park - a place where everything should be perfect and fun; also loss of the illusion of perfection), his absence implies that he neglected his job in favour of back-alley dealings to provide for his son's medication and his wife's drugs, and also the loss of friends and family without him noticing it - Japhet taking over Valerie without the Judge realizing it, and the Batter killing Japhet/Valerie.
The purification of the third zone is the loss of the source. Sugar is made from corpses - Zacharie is literally going over corpses to fuel Sugar's addiction.
If the Batter kills Sugar, Zacharie responds with "... I suppose it's better this way", even though Zacharie and Sugar are implied to be at least close friends in the game, Zacharie should be distraught and attack the Batter, but instead he is resigned, as if he'd seen it coming.
His continued support of the Batter via items for purchase (which cost more and more, because Zacharie has only this source of income any more and still tries to support his family) might hint that even if he couldn't save his wife, he will continue trying to save his son.
The Queen, as an imagined entity, can't replace the real world / affection Hugo needs, and as such, the world she creates is incomplete and can't sustain itself in the long run.
The game is literally Zacharie losing everything - if the Batter dies (Zacharie forces himself to stop), all that will be left over will be a world empty save for him and the Judge, and maybe Sugar, whom he can't support any longer, the Batter succeeding is Zacharie self-destructing after his son has died because of his own shortcomings.

This is also why the only solution to winning this game is not to play it: Because the only way not to lose down that road is not to follow it.