Also, beware, if you care about spoilers, there will be some for some of these theories. So if you care about the secrecy of plot points in games from 20+ years ago...beware!
The Pokemon War
But, one small comment made from one of the gym leaders spurred a theory about what happened to Ash's father. In Vermillion City, the gym leader Lt. Surge makes an offhanded comment about how "electric Pokemon saved him during the war". Considering that Surge looks relatively young, it could be speculated that whatever war he was in has not been over for very long. Now if there was a war, perhaps Ash's father had left and never returned possibly being a casualty of it. Why Ash's mom would let Ash go on a journey with Pokemon after losing her husband doesn't seem to fit with it particularly well, but at least it seems like a somewhat plausible explanation.
Plus, it makes me want a Pokemon game set during a war time. Imagine a war scene with Dragonite and Charizard soaring overhead while ground forces of Rhydon's, Rapidash's, and Onix's crash into each other on the battle field. Seems like such an awesome setting that we'll never see.
Gary Oak Seeking Clarity
Gary was a headstrong turd in Pokemon Red and Blue who was made out to be your rival. You battle him on many occasions, one of which is in Vermillion City. Gary, like some players, usually kept the same Pokemon in his lineup for a chunk of the game. But there was a point in the game in which you visit Lavender Town, or as most people would remember it, the town where Pokemon souls go to rest in Pokemon Tower.
When you battle Gary in Vermillion City, Gary has a Raticate. When you see him and battle in Lavender Town, that Raticate is no longer in his party and he makes some sort of cryptic remark about "Have you ever seen a Pokemon die?" And while it's perfectly reasonable to think he let the Raticate go or kept him in his PC Box, it seems somewhat weird that he would have one empty slot in his lineup and no longer sport one of his early Pokemon while keeping the others.
So why would he be in Lavender Town? Well, the theory states that when you battle Gary on the S.S. Anne, all of his Pokemon faint. Due to difficulty of getting off of the ship in time, he wasn't able to make it back to a Pokemon Center before his Raticate died. Perhaps it was injured worse than the others or it had some weird disease, who knows. The point is, that one Pokemon died while the others didn't. So he traveled to Lavender Town and paid his respects to his fallen Pokemon.
So now Gary is on a mission. To go out and beat Ash and prove he is a better Pokemon trainer while getting some revenge on Ash for killing his Pokemon.
Missingno Destroys Everything
I swear this is the last Pokemon related theory. But for those who remember playing Pokemon and taking a chance ruining their save file by capturing the elusive Missingno glitch, this is for you. For those who didn't know the pleasures of infinite Master Balls or Rare Candy's using Missingno, here's how it worked:
In the north part of Viridian City, a man will ask if you are in a hurry. You're not, so you tell him no and watch the demonstration that will benefit you in no way at this part of the game. Fly to Cinnabar Island or Fuchsia City (then surf to Seafoam Islands) and surf along the coast of the beach. Up pops Missingno. If you capture it, one of two things occur. Sometimes, your save data will mess up. BUT, the other thing can be a replication of the sixth item in your bag. Master Ball, Rare Candy, doesn't matter get replicated many many times.
But what is Missingno? This is where the theory comes in. Some say it's the code that allows a Marowak to transform into a Kangaskhan (meaning that Cubone is a Kangaskhan baby wearing it's dead mother's remains as mentioned in the Pokedex). But the theory that I love is that Missingno is a shrunken sprite of the Kanto region map. Meaning that when you battle and capture it, essentially, you are bringing into existence a Pokemon who is an alternate version of the world that you are in. And when you bring an alternate version of that world into the same place and time of the one you are in, that causes problems to reality. Which in a weird way can be construed as...a glitch.
But then who is Tabuu? Some crazy father who doesn't like how the boys play, so decides to wreck them his way by being a little too hard on them. The kids don't particularly like their dad, so of course he is the evil character in the game who happens to use the villains for his own deeds. But taking him out of the equation, it's just some harmless fun between two brothers playing with their toys. By smashing them. Superbly. Super. Smash. Brothers.
Of course, if you don't like that, you could always go with the Valhalla idea where all of these characters have died and are transported to the Viking mythological land of Valhalla. Where they battle each other in epic battles for all of eternity...
Mario is a Villain
This isn't anything revolutionary by stating that some theories have Mario as a villain. He's kind of an ass to everyone including his brother and Yoshi, he constantly lets the Princess get kidnapped, he's imprisoned Donkey Kong, and let's not even discuss how everything in the Mushroom Kingdom (like the blocks) are toads having been transformed using magic from King Koopa as stated in the Super Mario Bros. manual.
So the theory is slightly expanded on a little more by taking a look back to the Super Mario Bros. game. Take a look at the world. Sweet and peaceful. Turtles and Goombas, not doing a damn thing but walking around. That is until Mario runs around shooting them with fire and jumping on them or kicking them into each other. The world itself seems to be just fine until you get into further stages.
As the game progresses, the enemies also seem to get a bit more fierce. You have the Hammer Bro's tossing around their work tools, Bullet Bills trying to convince you of gun control in the Mushroom Kingdom, and Lakitus tossing around Spinys hoping to murder Mario from above. So if there is this crazy man running around killing people in your kingdom and conquering castle after castle, you beef up your force and try to stop him. Unfortunately in Bowser's case, he fails miserably.
Princess Peach gets kidnapped by Bowser though, right? Well, what if she is trying to get away from her abusive ex-boyfriend Mario by seeking refuge with Bowser? Maybe the only reason she goes with him at the end is to avoid being slapped around by her plumbing psycho ex so she doesn't avoid ending up like Pauline (who mysteriously vanishes...). So perhaps instead of Bowser being the villain, he's just trying to rescue Peach from this abusive relationship only to be manhandled by the two brothers. Because let's face it, Luigi is a moron and probably thinks his brother is doing the right thing.
And he convinces everyone he did the right thing by putting on a stage performance from his "perspective" in Super Mario Bros. 3. Only Bowser, Princess Peach, and Mario know the truth. Other than poor Pauline.
Squall is Dead
This one isn't as much fun because it falls under another cliche used in storytelling not reserved for just RPG's, even though it is one. Everything is a dream. Or in this case for Squall, a dream if one dreams...IN DEATH!
At the end of Disc 1, Squall and the gang is trying to assassinate sorceress Edea who is guilty of creating hostilities in their land. This ends up as horrible as it can go when Squall receives a large chunk of ice straight through his chest. He then falls while closing his eyes as Rinoa reaches for him, and cut to black.
Disc 2 starts out with him waking up in a cell with no memory of what happened between the Edea attack and where he currently is. The hole from the ice shard is gone and nobody seems to mention this fatal attack again. Some think he was healed by Edea before being captured, but there would really be no point in doing so.
The site Squall Is Dead really nails the point home, but some points they touch on include the absurdity of the story from that point on (Moombas, weird twists like Cid and Edea are married and that the man behind Balamb Garden is not human, and Seifer's relationship with Rinoa becoming almost nonexistent from that point) is one of them. They focus on some dialogue that can insinuate something deeper happening, and they even have a breakdown of what could be happening in the end game cinematic. I know I sure as hell couldn't tell you what happened in it when I first watched it, so I am automatically assuming that their explanation is truth.
So if you don't mind feeling that the majority of Final Fantasy 8 is a dream sequence that Squall is creating as he's dying in an attempt to wrap up his own story, than this may be the theory to cling on to.
Rinoa is Ultimecia
Supposedly Square has denied this theory as truth, but it doesn't make it any less interesting in a game most people tend to dislike, one reason being for the characters.
During the game, Rinoa becomes a sorceress and fears for the potential outcome. After seeking advice from Edea, she finds support in Squall since most sorceresses tend to go crazy. So Squall is her emotional tether to remain sane. Fast forward to the future where Squall is dead and Rinoa has gone batshit crazy becoming the time compressing sorceress known as Ultimecia. And time compressing is her method of being reunited with Squall.
Some points used to solidify this theory is that Ultimecia has the Guardian Force Griever which is the symbol Squall has both on his necklace and the ring he gave to Rinoa. Before the final battle, she mentions that she's attaching it to a character, so it can easily be Squall's Lionhart, but for the sake of the theory, we'll say it's the ring. Which in her mind, the Griever is her link to Squall. So when he died, Griever became her idea of Squall who "would always be by her side".
It's also worth noting that Rinoa and Ultimecia have some similarities like being the only sorceresses with wings (Rinoa-white, Ultimecia-black) and that they share similar facial structures which is reinforced in an FMV sequence which has the faces flash between each other.
Also, since the power she gained was the evil Adel's, she may have been tainted by his evil but been able to hold it off while Squall was alive. Once he died, the evil fully manifested itself and took over control of her entirely. And as for why she wanted to kill Squall, it was mentioned that the use of a GF can erase memories, so it's possible that she forgot who she was after using Griever.
Giygas is a Fetus
While it's more plausible to believe this theory as a symbolic interpretation over a literal one, some take this one a tad further than others.
At the end of Earthbound, you face Giygas, a being who loses mind and body due to being the ultimate force of evil in the universe. The way to solve this was by being put in "The Devil's Machine" which allowed Giygas to retain his power and part of his mind. And this is where the theory begins...
To some people, the machine Giygas is trapped in resembles a uterus with parts of it that could represent a cervix, vulva, and vagina. And what it holds inside is released once the machine is turned off, and the form surprised some people by looking like an outline of a fetus. Others have joked about seeing an outline of a duck and Mickey Mouse, but as outlined in the above picture, it looks pretty close to a damn fetus. Itoi has come out and said this was just a coincidence and not intentional, but people still run with it.
But...let's stick with the possibility that Giygas is a fetus. If his mind and body were destroyed and then put into the devil's machine, it could be trying to recreate a new body from the chaos (and thus) starting out as an infant. The evil tortured face that is shown in the fetus head and body could represent the evil still flowing through it. And it's choosing the form of an infant due to it's relation with Maria from the first game who took care of Giygas.
Plus, considering how weird Earthbound can be, would it really be that off the wall to picture yourself fighting an evil fetus at the end? Especially when the villain was created from a misinterpretation of a movie Itoi accidentally saw as a child making him think he witnessed a rape scene. Then trying to use the feeling he got when seeing that movie to incorporate it into this character and dialogue used.
There are some fans of Earthbound who absolutely HATE this theory, but whether it's as farfetched as they make it out to be...
Mass Effect Indoctrination Theory
Another game. Another cliche. Another dream. The Indoctrination Theory was the saving grace for Mass Effect 3 fans trying to gather some sort of ending that they thought was more appropriate than the ending they were given. It was their attempt to clear up some confusion and make sense of what exactly happened.
Which is to say, the ending may or may not have happened. Everything was in Shepards head. As Mass Effect pointed out many times during the series, Shepard is unique in being able to withstand the Reaper probing to manipulate the individual when so many have failed before hand. And Shepard has touched or been around quite a bit of Reaper stuff in these games, so he should be walking hand in hand with them near the end.
In the theory, he was. He was indoctrinated by the Reapers and everything that was experienced was a dream or hallucination. The way to break free from this control of the Reapers is presented by the three choices at the end of the game. If he chooses the blue (control the Reapers) or the green (synthesis), the Reapers inevitably win by still being a part of the universe. If Shepard chooses the blue, he can control the Reapers who in reality already control him. It's him giving away his free will entirely. With the green, he let's the machines be apart of every living thing in the universe which sounds like an end goal of the Reapers anyways. But there is the red option in which they are destroyed. The option for him to break free from Reaper control. Which, if selected, the player will see an extra scene at the end of Shepard coming back to life or "waking up" from the hallucination.
This would also explain why so many people were confused by the color options and why the outcomes didn't seem to match with the paragon/renegade color scheme the rest of the series portrayed. But, if the Reapers did have control of Shepard, then they would flip flop that and try to convince him that the bad/red option is to destroy them and you really want to select one of the other ones. It goes completely against Shepard's role in the series, but it would make some sense. And, if you look at it that way, the game is slightly meta by bringing the player into it and saying "you are indoctrinated as well...Can you break free?"
The folks on the Bioware boards put up quite a bit of evidence to explain how this theory makes the most sense, and it makes quite a good read. Especially if you were not happy with how everything turned out in the first place.
Chell is the Daughter of GLaDOS
Portal was one of those games that nobody expected to come out of thinking there would be this elaborate thought provoking story. It seemed like an innocent little puzzle game until suddenly BOOM, everything changes. But despite all of the changes, there had always been things not quite explained such as Ratman and who Chell was exactly. Some things did get explained such as who GLaDOS really is and the story behind Ratman, but Chell is still a mystery.
Like pieces of a puzzle, people have tried to fit a story into explaining who Chell is. And one of the most convincing ones out there is...she is the daughter of Cave Johnson and Caroline (GLaDOS).
So a little piece of fan fiction to elaborate on why this is. Portal 2 fills in a lot of holes such as Cave Johnson being the man behind Aperture Science who falls in love with a woman named Caroline. He gets sick and knows he will die and wants to leave something behind. His science isn't enough, although he uses it to make Caroline live forever in GLaDOS. But he wants a child. Someone his legacy can fall to when he is no longer there.
What happens can be split two ways. One is that Cave and Caroline conceive a child in Chell.
That's a lot of "C's" in that sentence...
The other that I'm more fond of and going to explain a bit more is that Cave and Caroline don't have a child, but adopt. And the adopted child is an infant Chell.
In Portal 2, GLaDOS makes an offhanded comment about Chell being adopted. It comes off as a personal insult like she was prone to do in that game. But later on, she remarks to Wheatley "What's so bad about being adopted?" Perhaps, this is her true feelings coming out letting Chell know that being adopted isn't bad, because her adoptive parents would still love her. That being, Cave and Caroline.
Chell was also a kid of someone at Aperture Science who arrived at "Bring Your Daughter to Work Day". Which would fall in line with her being the child of Cave and Caroline. But like Chell, we don't know the last name of Caroline either. Both of the last names have not been given and in Chell's case, her last name was "redacted" from her paperwork. It seems like Valve is actually hiding her last name, but since we don't know any other Aperture Science workers, what would be the point? Why have a last name at all, or just give some random last name? Perhaps because it matches the same last name of one of the 3 characters we know in the game. Cave Johnson.
Then there are little things like the turret opera lyrics sing "My child. My dear dear child", the link between GLaDOS being a potato and a potato being what Chell had brought in as a kid, GLaDOS saying she loved Chell in the first game, dates of events seem to match up, and GLaDOS mentions two relatives with the same last name being in stasis (and who better to keep in stasis then the big man himself and the love of his life?)
It goes on and on, but reading the theory convinced me that Chell is the daughter of Cave and Caroline.
Aeris Lives!
And quite possibly the most famous theory, Aeris was supposed to live in Final Fantasy 7.
Most probably know this one, but for those who don't, Aeris dies. Stabbed in the back by Sephiroth right in front of Cloud. One of those tear-jerking moments that caused an entire fan base to hate a villain like no other. So when they started hearing rumors that Aeris could be alive, the game was picked apart to support this theory.
Parts of this theory have been proven false. One included treating Tifa like crap and being nice to Aeris. Never have Tifa in your party. Go on a date with Aeris at Golden Saucer. Stuff like that. In the cutscene where Aeris dies, Tifa is supposed to push her out of the way (as long as she is in your party) and be killed instead of Aeris. Doesn't happen.
Another was that Aeris's final Limit Break is only accessible after she dies. This is not true and can be found with a simple Google search. Her ghost was another example that she should return, but her ghost appears to be a weird game glitch as her ghost can be seen on Disc 1 in the church after she is captured by Shin-Ra, but before she actually dies.
So where exactly does this theory come from? There are two biggest arguments that I have seen. One includes the picture above which comes from the manual. Aeris is shown standing in front of the Highwind, although the airship isn't available until after she has died. The second is the lone cliff at the end before the fight with Sephiroth. If you gather all of the allies (including Vincent and Yuffie), every ledge is accounted for by a character except one. Supposedly, this is where Aeris would have stood. Then during the final battle, when you must split into three parties, one of the parties only has two members.
There is a way to bring Aeris back, but it involves using a Gameshark usually. But the talk of the Internet had lots of grinding as the solution to bringing Aeris back. This included having her final Limit Break, leveling up a Cure Materia to receive the "Restore" spell, and receive the Underwater Materia used to cancel the timer for the Emerald Weapon fight. All of this needed to be done before she left the party to her ultimate demise. Then and only then would this work.
While it does seem there is no way to bring her back without a cheat device, that hasn't stopped the discussion about whether or not she was originally supposed to. While the creators have said she was never supposed to have survived, people who use a cheat device have found unique dialogue that only Aeris will use. Most of these are when she isn't dead yet, but not a possible character to have in the party. Some suspect that means the story could have been re-written including the part where she dies. Could mean she was supposed to die at a different time, or maybe not at all. Even though this shouldn't matter at this point thanks to the movie and spin-off games, some people can't let this one go.
About the theory "Squall is dead", in my opinion... Squall not dies in the game. (spoilers) If he die on Disk 1 everything that follows from disc 2 onwards would not make sense, we would not know the role of Edea, the connection with Laguna, Ellone, etc.
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Now, I want to mention the point "Just stay close to me."
There is a translation error in english version: "If I didn't, I wouldn't be talking about it." In the japanese version is: "If I did I couldn't talk about it like this", then she no longer likes Seifer.
See: lokasenna.pe.kr/ardente/etc./
One more thing, the line:. "I wonder how he felt...?" if I am not mistaken in the Japanese version is: "I wonder what he thought of me", indicating further that among them there was more friendship that anything else.
Speaking as what is presented here, she does not see to Seifer on the dance floor (actually he was not there), but she see at the director Cid Kramer and talk with him. This is indicated in the "Rebellion Princess" page, a page that brought information of Ultimania and other sources.
Also, Rinoa in the game NEVER says and ensures that Seifer was her boyfriend, then obviously they were not boyfriends. It is also important to say that she THOUGHT loved Seifer, NOT assures us even hinting several things: that she was confused with his feelings (for me the most reasonable choice), he was not interested, I had no desire to formalize a relationship with him, etc.. And to top Seifer did not know if some feelings / what he thought about her. I said, Is that a relationship? For me it definitely is not. where there is doubts, miscommunication (and precisely Seifer is not a silent type).
They only had a relationship purely business, hence Seifer falls in the summer with the Owls of the Forest, and he has a dream to meet a child (Rinoa is not a witch when he met, so it makes sense that he are not interested in her), and apart is a revolutionary type, who loves battles, for he delighted to release Timber, and continue increasing their ego.
If Seifer risked his life by Rinoa can not say, do not forget that he never says why, will not know your reason, but remember that Squall is also there, and he is his rival. Seifer fears that Squall and Rinoa are defeated for all the army of Galbadia majority and experience, and that's why going to his aid.
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Squall does not die in disc 4 (spoilers) because the the video where Selphie and Irvine filmed the celebration after beating Ultimecia, everyone is happy, that means that everything went well (include Squall alive).
Also, Kitase in the interview in the Ultimania says that in the game there is a happy ending.