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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Pokémon: Genesect and the Legend Awakened
aka: Pokemon Extreme Speed Genesect Mewtwo Awakens
    The New Mewtwo 
Identity
This Mewtwo is the same Mewtwo that debuted in the very first movie.
Judging by the latest trailer with Ash calling its name.
  • Jossed. It is a different one.
  • (Later Theory): Being a being of incomprehensible intelligence and physic power, it can probably change it's mental gender at will.

The Mewtwo in Mewtwo's Awakening is a different Mewtwo than the one in the first movie.
In the manga adaptation of this movie, Mewtwo had a different backstory, and it also speaks in a very feminine voice, in contrast to the previous Mewtwo's masculine one.
  • Confirmed. It is different.

The Mewtwo in this movie is cloned from the Mew from Movie 8.
What fans tend to forget is that a second Mew was already introduced into the anime's canon; therefore, it's possible that the new Mewtwo is cloned from it rather than Movie 1's Mew or a generic Mew that merely exists for the backstory.

There are 3 Mewtwos
The first is the original Cinnabar Island one in the games, the second is the New Island one in the First Movie and the third is the one in this movie.

Origins
The Mewtwo in the film was created because the original Mewtwo erased Team Rocket's memories.
Team Rocket created Mewtwo because they found a sample of Mew. If they had no memory of creating Mewtwo the first time they'd try creating Mewtwo again and since it's their scientists (Dr. Fuji is nowhere to be found since he's dead) making the product their Mewtwo would sound closer to Mew whom Mewtwo is based on. And since this Mewtwo never met any other clones it merely has distrust of Humans instead of outright hatred.

The events in Pokemon Mewtwo Returns did not expunge all records of Mewtwo's existence.
Think about it: Mewtwo used his psychic powers to wipe Giovanni and pal's memory of his and Mt Quena's existence, but there's nothing saying that he wiped out whatever records of him are left. Even though a lot of what's known about him was blown apart when he escaped, Giovanni probably has lots of super-secure files on Mewtwo. Giovanni and his Executives are the only ones who had files on Mewtwo. While Giovanni can't remember the password and place, the importance of the Mewtwo project(to the point that his own mother was part of it) would leave a colossal, mutant feline-shaped hole in the records. Having scientists brilliant enough to make Mewtwo in the first place find out what's going on, Giovanni rediscovered Mewtwo's existence. The reason Giovanni isn't going after Mewtwo again is because he's Genre Savvy to wait it out and ensure Mewtwo is in his command, especially now that he can't use his morality clones against Mewtwo. Unknown to Giovanni, Team Plasma managed to hijack this information and use it to create the Mewtwo in the 16th movie.

Anime Team Flare created Mewtwotwo.
How anyone officially got the data, we may never know, but Team Flare is said to do what they do for money, and even with what Mewtwo did at the end of the first movie, the fact remains that there was an explosion on New Island.

If a guess could be hazarded as to how, they probably hustled it & went there while Giovanni was conspiring with & deceiving Mewtwo elsewhere, and may have discovered some sort of DNA leavings either within Mewtwo's tube or where Mewtwo was standing...somehow. Or maybe one of the computers wasn't completely destroyed. The Mew screen may even be extra DNA they found in the strand.

Continuing on this, a movie where both Mewtwo appear will have Team Rocket and Flare gang up.
And both Mewtwos will have to join together to stop them. In a twist, Team Rocket may end up allying with one of the Mewtwo when they realize Team Flare's plan is batshit insane.
  • The Mega Mewtwo X/Y and Lysandre cameos in the "Strongest Mega Evolution" special lend some credence to this theory. The special (or possibly movie) would probably be part 2 of the miniseries, and seeing as it had a small amount of Pandering to the Base for the older fans, this could happen and Team Flare could be as dark as in the games. However, remember that this is the Pokémon anime. We could be just as likely to have some sort of cop-out special where only Newtwo appears, and Lysandre's plan is simply to awaken Xerneas/Yveltal to rule the world a la anime!Ghetsis.

Continuing on both of the above, Newtwo will make a reappearance and she will be shown to be connected with Lysandre and Team Flare
This could rescue her from the scrappy heap, as she would then be given her own interesting and unique story with a recognized villainous team from the newest games, establishing her as more than a shallow copy of the old Mewtwo. And of course, this would tie in with the Mega Evolution specials, which already show that the writers are willing to break formula a little.

The scientists who created Mewtwotwo are (or are connected with) "the other group who inquired about the legendary Pokemon years ago" mentioned in Pokemon X and Y.

Interactions
Mewtwo (in general) is a preevolved form of Mew
How else could one explain that two scientist groups using two different procedures in two different environments using two different samplesnote  end up with two specimens where the only significant differences are biological sex and the ability to use a Super Mode? The easy way to get such results in game-canon is by breeding. And there is precedent for such: Phione.

One distinguishing factor: the old Mewtwo's Ability was Pressure, while the new Mewtwo's Ability is Unnerve.
The event distribution says it all.

Ash remembers what Mewtwo is...
...because his Aura capability prevented Original!Mewtwo's memory wipe from taking hold.
  • Or, it could be the fact that Mewtwo didn't erase Ash's memories the second time they met.

This Mewtwo is in love with Ash
  1. it wouldn't be the first time a pokemon fell in love with him.
  2. It stops fighting the Red Genesect only when Ash asks it. Only interfering when Genesect attacks again.

Meta
Newtwo will become a Creator's Pet
Not wanting to accept defeat and admit that they made a poor marketing choice in creating Mewtwotwo and handling her character the way they did, Yuyama and the rest of the anime's creative team will decide to make sure that she becomes the "go-to" depiction for Mewtwo from now on - after all, Yuyama said his goal was to create a "new image" for Mewtwo. This'll likely result in her appearing in the next Super Smash Bros. (thus acting as the old Mewtwo's Replacement Scrappy again), and future depictions in other spinoffs and other media being based on her personality rather than the original Mewtwo. And their logic will likely be something like "today's kids will grow up with this Mewtwo, so they'll remember her for years to come and eventually she'll be more famous than the old Mewtwo, which we don't like anymore for whatever reason".
  • Greninja speaks in Pokémon Speak in the new Smash, which pretty much deconfirms the Origins versions of any Pokémon - including Mewtwo. If "relevance" and "timing" are factors, then that more popular Mewtwo would have been an alternative to this one. Cue Oh Crap...
    • Less of an Oh Crap when one remembers Game Freak calls the shots related to Pokemon, not Oriental Light & Magic.
      • Jossed (so far). Not only is Mewtwo (in general) not playable, but its trophy description seems to want to have as little to do with "Femtwo" as possible. This is probably part of a trend where official materials are trying to bring Mewtwo back to its ferocious Blood Knight roots, starting with Pokémon Origins.

Mewtwo was originally planned to be the original, but the writers changed it to sell more Mewtwo toys to little girls.
Notice how the event Mewtwo associated with this movie has Hurricane, a move most likely based on the first movie rather than this one. It's quite likely that the writers, looking to shove as much merchandise as possible, decided that Genesect was enough for little boys and that there weren't enough cute girly Pokémon in the movie to appeal to little girls, so they decided to make Mewtwo into one. And as for why she has nothing to do with the old Mewtwo, it's all part of the same package.

The original Mewtwo will make a return in a future movie as Mega Mewtwo X
... In a showdown against this movie's Mega Mewtwo Y. And this is gonna be awesome!

Alternatively, another Mewtwo will appear to showcase Mega Mewtwo X
Because this movie shows that the writers (or the director, more specifically) can say "screw continuity" and expect to get away with it if they feel like it, and as such they would likely rather have a third Mewtwo beause they think it would be better that way. Oh, and don't expect much of an explanation for a third one's origin, either.

New Mewtwo will have its own TV Movie sequel.
Old Mewtwo got his own sequel with Mewtwo Returns, which was used to placate fans pissed at the ending. History could repeat itself with New Mewtwo getting a movie explaining where the hell she came from, and even having old Mewtwo!

For the fangasms, there will be a Continuity Porn with all Mewtwo.
Not just the old and new Mewtwo appearing, but the Mirage Mewtwo, the Genesect and Mew. Hell, let's add Porygon for the fangasm!

A second Mega Mewtwo Y will be shown in order to make it more popular with Western fans
This movie turned a lot of Western fans off Mewtwo Y, so they could depict a second one in non-game Pokémon media to try and win fans over. It could be the original Mewtwo (switching between the X and Y forms like Kyurem did in its own movie), an Origins-like Mewtwo, or possibly Mewtwo's Final Smash in Super Smash Bros. for Wii U/3DS (provided they don't base it on Newtwo after all).

    Other Theories 
This Movie will showcase a Gen VI Pokemon.
At least one as a preview to the next generation.
  • Surprisingly, Jossed!

This movie will end with all the Genesect turning out as Not Evil, Just Misunderstood.
Between the manga showing the four purple Genesect doing a Heel-Face Turn, the Army's "we want to go home" motivation and the turnout of Mewtwo, Deoxys, Darkrai, Giratina and Kyurem's seemingly villainous appearance/roles prior, not to mention the animé's tendency to throw around "evil Pokémon don't exist", this is bound to happen.

Douse Drive Genesect was originally Snowdrop.
They both have a similar voice and personality. In fact, Douse Drive Genesect has a strange fascination with white lily pad flowers. Could this be Snowdrop trying to remember her previous life?

Pokémon: Giratina and the Sky WarriorWMG/PokémonPokemon Future Films
Pokémon: The First MovieWMG/Anime & MangaPokemon Future Films

alternative title(s): Pokemon Extreme Speed Genesect Mewtwo Awakens
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