From that point on, Naruto went to train with Mewtwo after class every day. After figuring out how to channel chakra to the brain to unlock one's psychic potential, Mewtwo taught Naruto a multitude of techniques known in his world. Psychic techniques were his specialty, from "basic" mind-reading to a variety of attacks.

Not wanting him to over-specialize, Mewtwo also taught Naruto some physical techniques and cover what he could from other types. Apparently some of them were near-impossible to chakra-using humans (Mewtwo was surprised to learn most Grass and Ice-type attacks were only possible for a few extinct bloodlines), but he taught what he could. Of course, seeing how most of the village already hated Naruto, Mewtwo insisted he "play down" his psychic abilities so as not to rouse any fear or suspicion. There were a few close scrapes, but nothing Mewtwo couldn't fix with a quick memory wipe...

Mewtwo initially only used the training as a means of using the Nine tailed Fox's chakra to unblock his memories, and on that front he made some slow progress (apparently just before he had awoken in the Hidden Leaf, he had been targeted by a trainer who had already captured several Legendary Pokemon, how this had lead to him ending up in another dimension though...) However, it wasn't long before he actually saw Naruto as his student, rather than a tool to find out what had happened to him and how he had gotten stuck in this world.

Not like my own world ever accepted me anyway...

It was now five years since Naruto started training with Mewtwo. Naruto had just graduated from the ninja academy. He had actually failed the final test (unfortunately, nothing Mewtwo taught him was on the test.. .) , but one of his teachers, Mizuki, had approached him after school about a supposed secret method of graduating involving taking a scroll from a top-secret vault and learning a jutsu
from it. He clearly didn't know Naruto could read his mind (a technique Mewtwo had taught him) and when Naruto refused, Mizuki had attempted to steal the scroll himself. By this time, Naruto had informed Iruka of Mizuki's plans and they stopped him in his tracks. Naruto's Psycho Cut attack had even impressed Iruka enough for him to allow Naruto to graduate.

And now he was in class, waiting to hear who he would be on the same squad as.

"Naruto? What are you doing here?" asked a voice as Naruto entered the classroom. It was Kiba, one of Naruto's classmates.
"Only people who graduated are supposed to be here now", added Ino, another classmate.
"I did graduate", said Naruto. "See the headband?"
Naruto sat down, but was immediately pushed aside by Sakura, who wanted to sit beside Sasuke, the most popular boy in the class. Despite this, he seemed to do nothing but brood and ignore the fangirls.
"Hope I'm not in a team with him", muttered Naruto to himself.
"Squad 7", announced Iruka. "Naruto Uzumaki, Hinata Hyuga and Sasuke Uchiha".
Naruto groaned. Sasuke was the one he least wanted to be in a squad with, and he barely knew Hinata, owing to the fact that she always went quiet when he was around for some bizarre reason. He had asked Mewtwo about it, but the Psychic Pokémon had always ignored those questions.
So I'm not with Sasuke, thought Sakura. At least Ino-pig isn't either
"So Sasuke is in the same squad as the one girl who isn't crazy about him", said Shikamaru. "How ironic".
"Squad 8", continued Iruka. "Shino Aburame, Sakura Haruno, Kiba Inuzuka".
Sakura looked at her teammates with indifference, still disappointed she wasn't in the same team as Sasuke, while Ino made some remark about how she would hate to be in a team with Shikamaru.
"Squad 10", announced Iruka. "Shikamaru Nara, Choji Akamichi, Ino Yamanaka".
"You were saying?" said Shikamaru.

After that, the class was told to have a break for an hour before meeting their respective sensei. Naruto opted to use this time to fill in Mewtwo about his team.
"From the sound of things, you dislike the Uchiha boy", said Mewtwo.
"Yeah, Hinata's all right I guess", said Naruto. "At least I didn't get stuck with one of the Sasuke fangirls".
"An Uchiha and a Hyuga", said Mewtwo, more to himself than to Naruto. "Perhaps they thought your mind-reading was some form of Dojutsu, so it seems likely they made this team as a full squad of ninjas with ocular bloodlines".
"That sounds cool", said Naruto. "But I don't have any eye powers".
"That shouldn't be a problem", said Mewtwo. "Just try not to give the impression that you're a fool".

I split this chapter in two for the rewrite, it was probably the most rushed bit in the whole story. This part, I think, hints at some slight changes I'll be making to this rewrite and also fixes a few odd pseudo-plotholes of the original. Anyway…

New Instruments coming sort of soon!