So, also jetzt eine seeehr ausführliche (ACHTUNG) Zusammenfassung. Leider auf englisch...

So, you play a trainer, as usual. You start in a City and you've to go to a scientist. (we know all that :3) But then, he doesn't gives you only a Pokémon, he also gives to you a Quest: You've to catch mewtwo. You should do this with a Masterball, which is only created for Mewtwo in this case. But the City, where you can get the Masterball, is very far away. So you have to travel to there. On the way you've to fight Trainers/Pokémon, earn Gold. So but the important things now:
As you know , Mewtwo was created by team rocket. And in the beginning you get the quest from a Team Rocket Scientist. But the character itself doesn't know this. He thinks, its good to catch mewtwo (he gets money, etc. XD).
You've a Rivale too: Its Gary. He has a quest too (he also shall catch mewtwo) But he got the quest from Team Magma. They wanna have Mewtwo, to rule over the world, and that they have the most Power.
So after some time playing, you learn what Garry's aim is. Then You want to be much faster. So well, many adventures on the way to the city, where the Masterball is. But thats unimportant now.
Before you get to this City, you meat Mewtwo!! He's searching for answers, and feels lost in this world. (its not his place) Naturally he makes you forget everything, and then it turnes black in front of you're eyes.
When you're waking up again, you find out, that Mew has rescued you and took you to this place. Its Mew Island. xD
After some happenings Mew tells you the truth: It tells you all about team rocket and team magma and you recognize your terrible mistake. So in the end you want to get the Masterball to destroy it, and Mew says it will company you. You also want to stop Garry and warn Mewtwo. (for Destroying the Masterball, you need some special kind of Item. I don't really know which one exactly, I'll think about it XD)
You get the masterball, but you don't find garry, so you're searching this special Item first. Many Adventures again. XD Team Rocket now learend that you're make fun of them and they send some members, for hindering you and getting the Masterball. -Adventures- Its a hasty chase. (By the way, Gary is angry, that You got the Masterball first and goes back to team Magma. He doesn't know anything about their plans.)
While this you get to Mewtwo and warn him.
...Erm, well... After some happenings I've to invent first XD,Team Magma or Team Rocket (or both of them, don't know) get you anyway. (Perhaps there are "pokémon-armies" too) They have such a machine like in Mewtwo Returns. >.>
So in the end, when everyone thinks it's over, Mewtwo've to die, and the world ends, you passes out again. But then you wake up: And look: Everyone's alive and there's no Team Rocket/Magma anymore. You wonder where you are, when suddenly a strange human enters the room, where you lies. You ask him, where you are and he answeres, you would be safe. After some blablabla, you learn that these humen have hightechnologies and that they're some kind of "supermen" (but no godess or angels). They've learned to communicate with every Pokémon only in Mind and they're some kind of linked to the Pokémon. Mewtwo talks very very much to them. You also learn , that they're catching every lost and lonely Pokémon soul, that it can live there and can be happy. (they can bring them to live) (with lost Pokemon soul I also mean a Pokémon, who's died, which trainer whas really nasty to him or it was lonely everytime.) The people there are really lovely to their Pokémon and especially to the "Lost Souls". (by the Way, this "humen" live in a parallel univers, created by some icognitos). Then you recognize, that there's Celebi in this world. It is some kind of patron for it and it saves the "humen" there from bad luck, as they sey. Celebi goes to mewtwo and brings him to a place where they are lonely and they can see the wonderfully twinkling Stars an the pale, but beautyful moon. When they're stading there something happens: Celebi transports Mewtwo back in time! Back to his "childhood" and he sees how he meats Amber. When she's dying, the big Mewtwo's also cryin and celebi brings him back. Mewtwo wants to know, why Celebi has done this, and then celebi says, that Mewtwo had to see this to understand, that not all humen are bad to him and that he could live not only secret with humen. celebi also says: "Look at the Stars, perhaps you're not so lost and lonely, as you think...", before it goes away. (perhaps there happens something other, but Im not quite sure) Mewtwo doesn't say anything first and stay at this wonderfull place, where you can see the stars and the Moon. He thinks about Celebi's Words, but feels some kind of lost Soul. (you can see this, cause you're watching it in secret)
I don't know what should happen now exactly. But there should be Amber somehow.
In the End Mewtwo stays at the parallel universe, because there's amber, and he doesn't want to leave her. So he has learned to like one humen. One single Human. But he likes her very much. So mewtwo stays, but Mew and you goes back to your world. There are the Teams again and want to catch mewtwo, but you tell them that he's gone. They can't beliefe, but after having searched for him desperately, they finally give it up.

And thats the story of how mewtwo learned to like humen.