The short begins in a deep, dark, tropical forest somewhere in South America. A few Mankeys scatter up the trees as a team of scientists dressed in explorer gear walk below. Mew hovers above them. It flies down to a leaf with a hole in it and watches from there. The scientists have no idea it’s present. The head scientist explains that today, his colleagues and him will reach the site where an ancient civilization built a shrine to Mew, the rarest and strongest Pokémon ever, now believed to be extinct. When they pass Mew, it leaves the leaf and follows. It hovers through a field of Butterfree and continues to watch the scientists.
The scientist then explains that when Giovanni, the head of Team Rocket, heard of his work in the field of cloning, he agreed to fund his research, but only if the scientist would create him an enhanced living replica of Mew. The scientist agreed, for Giovanni just wanted to control the most powerful Pokémon in the world, the scientist, however, wanted something more. They reach the site to discover that the shrine is there. It shows them take a few pictures before entering the shrine. They walk in to find a tablet on the wall with a picture of Mew. Suddenly, Mew’s shadow appears on the wall, then flies away. The scientists look back but see nothing there. The scientists are then shown entering their tent. The head scientist explains that his team has discovered what they believe to be a Mew fossil, and he prays it’s authentic. If it is, he might be able to make the most powerful Pokémon ever, and may be able to learn the secret of restoring life itself. Mew appears outside the tent and looks in. It then turns and heads for a huge mountain across the forest. The scientists are then seen at the lab, performing many experiments and genetic splicing. It ends the scene with a monitor of the DNA, following a tube full of liquid. A young Mewtwo awakens in a pitch-black environment.
He asks who is he, what is he, and where is he. It then shows the scientists looking at him through the tube. One of them explains that Mewtwo is just like all the others clones, who were all unconscious. Mewtwo then senses others near him, but he doesn’t know what noises they are making. Suddenly, he hears a voice of a little girl. She tells him that those are words, and that they are talking. Mewtwo asks who she is and a little girl materializes beside him. She tells him that she is a person. Mewtwo asks if he is a person. She explains to him that he looks like a Pokémon, but he can talk, and that she didn’t know that Pokémon could talk like people. Mewtwo is confused and asks if he is a person or a Pokémon, but she just tells him that it doesn’t matter to her. She then tells him that since he is there, he must be the same as all of them, and a Bulbasaur, a Charmander, and a Squirtle appear. Back in the lab, the scientists watch the screen. The head scientist asks what's going on, and the girl scientist explains that Mewtwo seems to be communicating with the others. The scene then shifts to the clones again.
The girl explains that all of them are copies, that’s why they all have 2’s at the end of their names. Mewtwo asks what she means and she tells him that they call her Ambertwo, but she is still really Amber. They float around in a circle as she explains this. In the lab, the head scientist is staring at the tube that contains Ambertwo, who is just a red light. He pleads that his cloning theories are correct so he can see his little girl’s smile again. He then has a flashback of him in his basement lab. His wife appears at the top of the stairs. He tells her that Amber lives within the light in the tube, and if his theories are correct, he could have her back soon. His wife yells at him, asking why he needs to do this. She says that their daughter is gone and he needs to accept it. He refuses. The next scene shows a note left on the table with a wedding ring and cars keys on top of it. The note is from his wife. It explains that she loved their daughter as much as he did, but no one can bring her back, and she can’t go on watching him try.
The note ends with goodbye. It then shows the scientist depressed in his basement lab. He gets up and puts his hand on the tube, saying he’ll do anything to bring Amber back. Back in reality, the head scientist is asking another how the clones are doing as they walk through a corridor. The other scientist explains that they are doing fine, and Mewtwo is getting stronger every day so one is bound to survive. The scientists walk into the cloning room. The head scientist informs them that Giovanni might had the most powerful Pokémon soon, but he will get something more...knowledge of how to recreate life. He will then use it to bring Amber back. The scene then shifts to the clones. Amber has taken them to a small neighborhood that she calls her remember place since she used to live there. Mewtwo looks up at the sun and asks what it is. She tells him that it is the sun, and it makes the world bright all day. They then fly through the sky some more. Suddenly, a light breeze blows and Mewtwo asks what that is. She explains to him that it’s the wind, and sometimes it’s soft and other times it’s very powerful. The sun then starts to go down and she explains that that’s the sunset. She says that is when the sun says goodnight and see you tomorrow. The moon then appears and Mewtwo asks if that’s a sun. She tells him it’s the moon, and all the little bright things are stars. They shine just so people don’t feel lonely at night.
Suddenly, Charmandertwo starts to sparkle. It dissapears and the scientists notice they are loosing all readings of the clones. Squirtletwo and Bulbasaurtwo also fade away. Amber then starts to glow. Mewtwo asks where they all went. The scientists tell the head scientist that they are loosing Amber too. Mewtwo asks Amber what is happening and she says it feels like it’s time to say goodbye. He feels something in his eyes and he puts a finger up to them and sees tears. He asks what they are and she explains that they are tears and he’s crying. She says that her father used to tell her a bedtime story that when Pokémon are sad, they cry, and their tears bring life. She then tells him she has to leave him now and that he shouldn’t be sad. She tells him not to cry because he’s alive, and life is wonderful...she then dissapears. Mewtwo tells her to come back. He then pleads for her too. The scientists look to see his brainwaves surging. The head scientist tells them that Mewtwo can’t remember any of this. They then administer 100 units of serum and Mewtwo’s brainwaves go back to normal. The scientists say everything is fine again, but the head scientist says nothing is fine. He has lost his daughter forever, and only Mewtwo survives. It then shows Mewtwo in the pitch-black environment again. He is slowing aging from infant to adult. As he ages, he says that it seems like he has slept forever, but he remembers someone telling him that life is wonderful...but why?

Thanks To GoldenNoctowl For Writing this for us

The Origin of Mewtwo

Mewtwo's Birth


Mewtwo Strikes Back

Mewtwo Returns