WMG: Metal Gear Solid 4: Guns of the Patriots

Drebin is Fortune's younger brother
Aside from the obvious fact that they're both Dark Skinned Blondes, imagining them as brother and sister isn't much of a stretch. Keep in mind, if he's Fortune's brother, this would also make him the son of Scott Dolph, the Marine Corps Commandant from Metal Gear Solid 2. If he's the son of a Marine officer and the brother of a professional terrorist, it's not hard to imagine where he got the skills necessary to make it big as an arms dealer. And by my count, this would also make Ocelot responsible for the deaths of two of his immediate family (for all we know, they're the only family he's got). That would give him more than enough reason to want to make Ocelot's life hell with his arms dealing business. It might also explain his fixation with Solid Snake, and why he conveniently turns up wherever Snake is — it's only natural that he would want to meet the guy who stood the best chance of avenging his family.

Sunny is a reincarnation of the Boss and her first friend seen at Meryl and Johnny's wedding is a reincarnation of the Sorrow.
Sunny and the Boss have the same voice actor, and both have known a Snake closely. The little boy who Sunny played with didn't speak English, a hint to how the Sorrow and the Boss were from different countries.
  • Alternatively, Sunny could be a clone of The Boss. Les Enfantes Terribles all over again, perpetrated by the Patriots just before the events on the Big Shell, with Olga as a surrogate mother.

Liquid Ocelot is Hideo Kojima
Consider; you have Liquid Snake, the flamboyant, showy, dominant side. That's Hideo Kojima, the young man who wanted to make movies, the one who fills his games with long, elaborate cutscenes. Then we have Ocelot; once just the same, but then crippled by change [the fall of the Soviet Union] and then by his own hubris [growing so focused on Snake he lost a hand to Grey Fox]. Ocelot is Hideo Kojima, the older man who wanted to make videogames. You could view MGS4 as the struggle between his desire to give the fans a resolution to every plot issue, and the more thoughtful side that wants to make the game he wants, not necessarily the game the fans want. The fact that Ocelot's role is huge in MGS2 [where he did just that] and tiny in MGS4 [which was mostly for the fans, here's to you and all] rather gels with this. I wonder if he realises.

The Joy will make an appearance in MGS4
Hey, you didn't see Snake actually kill her in MGS3, and the Migs 'destroyed the body'. And of course, nobody bathed in that much napalm could possibly be dead. Come to think of it, maybe she's a Time Lord too, or Lady, as the case may be... which could mean she's actually already one of the established characters. Tying it in with the idea of Otacon being badass... Otacon is the Joy?
  • Didn't see him actually kill her? Did you miss the part where Snake put a bullet through her head with her own gun? Oh wait, you couldn't, because the game forced the player to pull the trigger in perhaps the most heartbreakingly interactive cutscene ever. I'm rather surprised a fan of the game could forget that. Of course, this is probably An April Fool's suggestion anyway.
    • Yeah, but the angle was wrong, there was no blood, and hey, we didn't have any depth perception at the time.
      • But Snake doesn't need depth perception, hes too awesome to be hindered by the loss of an eye.
    • It was mostly based on the idea of Unreliable Narrator and especially Never Found the Body, what with the napalm and all.
      • In fact, the napalm seems like a setup for just this. Why use it?

Solid Snake isn't in MGS4
We've played as Snake's fanboy, Snake's dad and Snake's clone, but the main man himself hasn't been a playable character since Metal Gear Solid. And the end of that game was a fine ending point for his personal arc. Why break the trend now?
Also, the trailers have demonstrated that the protagonist, whoever he is, wears a camouflage mask that can change his appearance. Clearly his real identity is:
  • Otacon, as mentioned above. What could be more fan-baitingly ironic than to discover that you're not playing as Snake, but playing as a fanboy playing as Snake?
  • Big Boss. He's appeared on a few promotional posters. He knows the moves. He's infinitely cynical about wars and causes. He would be about the right age, if he were still alive.
  • Liquid Snake. You think a little thing like FoxDie can stop him? He wants his hand back.
  • Decoy Octopus, impersonating Snake... All part of Liquid's plan.
  • Master Miller. Liquid Snake didn't kill Miller. He's Just Hiding. Miller faked his own death to avoid being killed by Liquid. Now Miller is going around posing as his greatest student, Snake (who is really dead).
  • Raiden. Again.
  • The Joy.
    • Or possibly the End. He's already over a hundred, what's a few more years? And this time he has a few technological goodies.
      • Or the End's clone.
  • The Sorrow. Solid Snake didn't survive the events of MGS2 because of Raiden's stupidity, and now Snake is being channeled by The Sorrow.
  • Rosemary. The Internet commits seppuku.
  • Some guy dreaming in V.R. In the future.
  • Hideo Kojima. Just to screw with us.

Solid Snake is in MGS4
He will be saved by mind uploading into an android copy of his younger self to become "Metal Gear Snake".
  • Hey, it's one sci-fi trope they haven't used yet. And that name is damn cool. Not to mention there's some tasty irony there.
  • If you use the Young Snake FaceCamo, especially w/ Bandanna, it's not only true (by being Solid Snake and not Old Snake), it's easier for you to pretend that it really is that android copy of his younger self, even though that's obviously not true.

Nanomachines don't do everything.
Oh, they could do a lot, don't get the theory wrong. It can definitely help regulate and control powers. But the primary reason the Patriots used nanomachines was to control bodies and minds. What better meme than to tell those with special powers that they are the ones who supply the power? That countering the nanotechnology "removes" the powers is an inverse of the Magic Feather phenom.

The "Snake" codename will be retired.
Big Boss dies saying "The world would be best without snakes." A new main character will be named Solid something, not something Snake.
  • And thus Saint Patrick's day was born.
    • ...the new character will have the real name of Patrick!

Ocelot made up the ridiculous thing about inferior recessive genes to manipulate Liquid and Solidus.
The Database and MGS4 only call Solid and Liquid imperfect clones. Also, this it totally Ocelot's style.

Every copy of MGS4 has a coating of nanomachines on the top of the disc, activated through touch, programmed to infect and give the player a Johnny Sasaki-like experience.
This troper is not kidding when he says he, with no warning, became violently, violently ill shortly after helping Rat Patrol Team 01, soiled Johnny included, fight through the wave of Frogs. Clearly, Hideo Kojima was worried that we would have a hard time being sympathetic to Johnny, not because he's unlikeable, but because of schadenfreude over his diarrhea. After ten hours of intense stabbing pain in the stomach, followed by nearly a full hour in the bathroom and repeated, random spells for a day afterward, this troper has gained an immense amount of sympathy for Johnny.
  • This troper would like to second this. While not nearly as bad, she had to make a big deposit at the brown bank (and she's leaving it at that, lest we get into Too Much Information territory) shortly after either that sequence or the scene where you first meet Johnny; she can't quite remember at the moment, but she's thinking it's the former.
    • This Troper hasn't yet played MGS4 because he doesn't have a PS3, but following a recent surgery that forced him to take anti-biotics with a side effect that can only be called "Johnny Sasaki Syndrome". Upon playing MGS1 after this incident this Troper tried to kill Meryl for what she did to Johnny.

Both "explanations" for Liquid Ocelot are true
Yes, yes, we all know by now that Ocelot used nanomachines and hypnotherepy to become Liquid Snake, as opposed to Liquid possessing him, at least according to the information that's explicitly mentioned. But let's read between the lines here, people. Keeping in mind that the former spoiler-tagged method is true, let's take a look at another MGS4 character, Screaming Mantis. She too had been given nanomachines and hypnotherepy to take on the personality of Psycho Mantis. And what ended up happening? Psycho Mantis' ghost ended up possessing her. Both Ocelot and Mantis' methods are identical, so logically the results should have been the same.
  • Alternatively, since Ocelot bothered to have Liquid's arm cut off and a prosthetic mounted, Liquid possessing Ocelot in MGS2 was genuine and Ocelot had the arm re-amputated after it became apparent how much of a problem it was, choosing instead to fake the rest of it.
    • Well, the MGS2 events are genuine; that much is said in the Metal Gear Solid database. I'm talking about the time after he had Liquid's arm removed. In any case, the result, under this theory, is the same: When Ocelot "faked" the possession, Liquid's ghost possessed him, much like with Screaming/Psycho Mantis (whether that was the intended result or not is debatable).

JD is the subject of the Judas Priest song Electric Eye
Up here in space \ I'm looking down on you \ My lasers trace \ Everything you do You think you've private lives \ Think nothing of the kind \ There is no true escape \ I'm watching all the time I'm made of metal \ My circuits gleam \ I am perpetual \ I keep the country clean

Solid Snake has a Shout-Out to Dawn of War in Metal Gear Solid 4
He has upgraded to hiding in METAL BOXES!

Vamp is still alive.
It's explained flat-out that Vamp's regeneration is a natural ability highly augmented by nanomachines. It's a reasonable assumption that he didn't get these nanomachines until after MGS2, just compare his scenes in Sons of Liberty to his scenes in Guns of the Patriots. In the former, mortal wounds like shots to the head drop him for a good long while. The head shot also leaves a permanent scar. It's suggested that he needs contact with water to regenerate, but this might just be symbolism of some kind. In the latter, however, he gets up seconds after a shot to the head, the wound closes instantly, and wounds from blades heal nearly as fast as they're made. The conclusion, then: what we see in Sons of Liberty is Vamp's natural ability, without nanomachines to help. Thus, injecting him with the nanomachines suppressor should simply put him back to this state, not remove his regeneration entirely. As such, Raiden was able to actually beat him in a fight, because now he can't raise instantly from anything, but that's different from killing him.

Of course, he has another problem; he's buried under several tons of rubble. And he'll probably be mightily pissed off if anyone ever drags him out. Then again, anyone who would drag him out after arriving at this conclusion might very well just want to set him loose in a specific direction...

  • There's also the little matter that Shadow Moses Island is sinking under the sea due to global warming. This means that, soon after MGS4's ending, Vamp is trapped under both a huge pile of rubble and an ocean, unable to move but unable to die... waiting.

Solid Snake's accelerated aging isn't due to the fact that he's a clone or because of his genetics...
It's all a lie. The reason he's aged terribly and has bad cardiopulmonary health is because he's a chain smoker. Still think smoking is cool, kids?

The Late June '09 rash of celebrity deaths? All FOXDIE.
Despite theories to the contrary, a constant string of celebrity deaths needs many more than 23 days to properly orchestrate and execute. Hence the use of FOXDIE as a smokescreen by the Patriots to lure public attention away from their 1500-page climate control bill, designed to control the amount of carbon humans can use as yet another extension of the S3 Project.

The BnB Unit girls' traumas didn't happen exactly the way they were depicted in the game.
They did suffer horrible trauma that drove them Axe Crazy in their various individual ways, but the Animal Motifs of their particular psychoses were instilled by hypnotherapy once Liquid Ocelot recruited them, as some sort of twisted tribute to FOXHOUND. Given that this is the guy responsible for Mount Snakemore we're talking about, it wouldn't necessarily be out of character for him to go to this much trouble over an issue of style, and even in the Metal Gear universe, it's a bit improbable that Ocelot managed to locate four young women who each manifested two traits from two separate, previous Quirky Miniboss Squads.

The Ending of Metal Gear Solid 4 was all a dream.
Snake died in the microwave hallway, the rest of the game was all a hallucination. The Patriots Demise was Snake's desire to see them destroyed before he died, Johnny and Meryll's Wedding was the life he failed to have after MGS1 (Supported since the other members of Rat Patrol are there...and they looked pretty dead at the end of Act 3), The scene between him and Big Boss was taking place at the pearly gates.

Dr. Drago Pettrovich Madnar did indeed die in Metal Gear 2.
The Dr. Madnar mentioned in MGS4 is his daughter, Ellen Madnar. We never see 'Madnar' in person. Perhaps Dr. Madnar is like Dr. Clark, somewhat of a recluse and rarely exposing themselves in person to others. Naomi thought Dr. Clark was a man as a result of this, so it's possible that this could be the case again. Dr. Madnar apparently did work strictly underground, so perhaps this is why she stayed hidden.

Raiden's... modifications... in MGS4 are similar in nature and root to that of the B&B corps
Just compare how they look. Not to mention that Raiden has the per-requisite "tragic war-related past" thanks to his child soldiering years.
  • Not to mention that he was a Bishonen Beauty before he became a Cyborg Beast. Now imagine Raiden shedding his exoskeleton to reveal himself wearing a two-piece, while posing for pictures and dancing to Oishii Two-Han Seikatsu. SWEET DREAMS KIDDIES!

Not only was Big Boss sexually attracted to boxes, but this was the driving force of the plot
As we know from Metal Gear Solid 4, the bulk of the series plot stems from various men and women having massive crushes on him that weren't reciprocated or even noticed. He didn't notice any of said crushes because he only has eyes for The Box.
  • He is, however, willing to have threesomes. As long as The Box approves.

Otacon was the Spanner in the Works necessary to defeat the Patriots, and his being so is a direct backfiring of what the Patriots had intended for him.
Here's what happened: Julie was a Honey Trap /Patriot plant meant to seduce both the Emmerich men, thus driving Huey to commit suicide (they no longer had any use for him) and causing Hal to think of himself as a worthless person (therefore a malleable one), as well as driving him to make something of himself. Through subtle planting and information monitoring (an inspiring teacher here, a cool robot show there), they created in him the desire to make super robots, a desire they knew they could take advantage of. Thus, he was the chief architect of Metal Gear REX.

As they monitored his interactions with the other scientists on the REX project, the Patriots realized that they could not remove his strong Neutral Good tendency and turn him fully into their tool. Nor, they realized, could they hide the truth from him for the rest of his productive life. Thus, their plan was to leak him the information about REX having nukes after its first successful deployment. Distraught by the notion that he was and would be responsible for a large-scale loss of human life, and feeling utterly abandoned by humanity, Otacon would then commit suicide, like his father before him. His attraction to Sniper Wolf ensured that he would be too distracted to discover just what was going on until it was too late. After his death, the Patriots would upload Hal's knowledge and thinking style into an AI, without that pesky Neutral Good alignment.

But they didn't reckon on Snake finding him in that storage locker.

Not only was Hal instrumental in defeating REX, he also saved Dave from a probable Despair Event Horizon after all of the events in the latter's life. The two gave each other a home, purpose, and love, thwarting the Patriots' plans to make them both useless through either death or severe isolation. Emma's death was intended to drive Hal over the Despair Event Horizon and make him abandon Snake and Philanthropy, but instead it made his will and bond with Snake stronger. Due to the education Otacon had received, not to mention his Emmerich genes, he was the perfect weapon against the Patriots. This cute little Otaku who wasn't supposed to live to his thirty-first birthday was the Patriots' greatest mistake and the key to their defeat.

Alternatively:

In reality, Ocelot
set up the Dave/Hal partnership both as the ultimate Anti-Patriots tool and as a way for him to vicariously achieve being with Big Boss.

The above WMG was what the Patriots thought was going on. In actuality, Snake and Otacon meeting was all part of the plan. Ocelot knew full well that they would bond and *cough*fall in love*cough*. In fact, he was counting on it. The two of them were planned to be the ones who took the Patriots down.

In addition, Hal was Ocelot's stand-in of a sort. His Ascended Fanboy tendencies were meant to be a mimic of Ocelot's own attitude towards Big Boss. The mostly-happy life that they built in those ten years was what Ocelot wished he had with Big Boss. Their happiness gave Ocelot a second-hand joy.

Mrk II and III are a new generation of benign Patriots, and everything was according to plan.
As You Know, Drebin and Rat Patrol 01 were both sent by the Patriots, to help ensure Ocelot's defeat. They simply didn't predict Foxalive. The catch is, however, they actually did. The Mark II and III show considerable personality when not being directly controlled, most notably in the ending, suggesting they have at least some level of AI. And who designed most of them; Sunny. During her time in V.R., the Patriots either directly or indirectly caused her to gain knowledge of AI creation, in addition to the rest of her computer skills, in order to allow her to create a Robot Buddy for Snake and Otacon. The reason for this being, that they realized they had gone off the rails. The were made to be safeguards to the world, and the War Economy was destroying it. However they could not go against their programming and resist the norms they had set, there was no other course for them. And so, they ensured their own destruction, and that it would be witnessed by a new generation of AI's. Who would learn from their mistakes, and the actions of the heroes, and use that knowledge to create a way for their "species" to help the planet without destroying it.

Metal Gear Online (2) is a depiction of the War Economy in action, mercenaries against other mercenaries.
Furthermore Liquid Ocelot participates in these battles because he is testing out his control of the SOP system. Everyone else is just a gameplay interpretation of the various battles that took place in the story, for example Raiden vs Vamp.

Snake is responsible for Sunny's mental/emotional problems.
Come on, he shot Sunny's mother full of tranquilizers while she was pregnant. That can't be good for a developing baby.

Drebin is actually Sigint's son
For starters, they share the same Japanese voice actor. Second, they know a lot about weapons and have connections with the Patriots. Screw the canon, this explanation makes more sense.

The AI doesn't exactly goes A.I. Is a Crapshoot, but more like Gone Horribly Right.
My theory is that the AI, at first, only acts as professional advisors and workers for things that nees massive works that needs high concentration and meticulity. They were built by combining (supposedly) Big Boss' and Zero's personality. Of course at one point in the past, Zero become vegetable, right after he input the AI's command as "amassing wealth through best way possible" for resources, "attempts single control at world's population", and, to honor Big Boss wishes (since he still considers him a friend, and The Boss successor), inputting command "create the situations where soldiers are always needed". The conclusion? War economy. The reason Sigint and Para-Medic didn't do anything can varied from simple greed to be unable to do anything (most likely, the control is solely on Zero) and decides to play along.

Snake's name was cleared as an insurance policy against Ocelot.
Philanthropy proved itself too dangerous before MGS2, so the Patriots framed them as terrorists. But Ocelot went Liquid on them, so they figured Solid and co. would work better as a Wild Card in the next stage of the Patriot Civil War. They pardon them from the accusations, but don't offer them direct support. This almost works, except that Solid still takes them down.

Sunny's new friend's name is Cher.
Well, why not have a groan-inducing couple name?

Fox Die and Liquid Ocelot
There's a plot hole with the fact that despite all the intimate contact between Snake and Ocelot after the new Fox Die strain is injected into him, Ocelot doesn't die until he goes back to his true self at the end. We know he was a target for the Fox Die so it should be his DNA sequence ... But he did take the vaccine for it. If that isn't true, the Liquid ruse was to fool the Patriots to send Snake after him the same way they did back on Shadow Moses ... And just like then they put in Liquid's DNA, and probably in place of Ocelots due to them not being able to tell the difference. "Liquid is causing trouble. He should be dead. Make him a target." "Affirmative JD, what about Ocelot?" "We lost contact with him a while ago. Presumed deceased." So he didn't die because he wasn't Liquid. Alternatively to that they programmed Liquid's DNA to trigger it expecting the transplanted arm to set off the virus, but didn't anticipate that the biological arm was removed long before hand.