Public review response:
To Seanhicks4: You asked me three things that I've been waiting for someone to ask, so here are your answers.
First, you asked "How does Shinji have the Sharingan?" That answer will be revealed at the end of the NERV arc, so you'll have to wait until the end for that one.
Secondly, you asked about the speed of Shinji and Naruto's training.
Answers:
Naruto's training speed is thanks to his new control of his half of Kurama that the Rinnegan gives him, allowing him to make more clones then his canon self which train off screen.
Shinji's training is because he can make as many clones as the canon Naruto and he learns quicker than Canon Naruto.
Shinji is just a quick learner and he also uses shadow clones to train; not on the same level as Naruto, but close.
Karin was already a trained shinobi. She just had to learn some family jutsu. Also, since while Kushina was still the whole version of Kurama's Jinchūriki, she has three tails worth of Nine Tails chakra. Like her brother, she uses shadow clones as well.
Now Rei is half angel, so controlling chakra, or, as she calls it, A.T Field energy, comes easy to her making her a quick learner.
Since shadow clones have copies of everything, the original was touching Shinji, using them to help Misato learn faster.
Finally, transfer and communication between the two worlds is not easy. Shinji uses his link to Eva-01's mind as a shortcut.
Itachi was able to travel to Shinji's world by using what was left of the rift that brought him there which took a lot out of him since it worked by feeding on his chakra.
When Itachi spoke with the other Akatsuki members from Tokyo-3, this also used a lot of chakra, but Itachi was strong enough to do it.
I'm really shocked no one else asked these questions, so, people, feel free to ask questions. I may answer you through a private message or, if I think it was a really good question, I'll reply to it in the next chapter.
Now, on to the story.
It had been two weeks since Shinji start training to do the Flying Thunder god jutsu. Naruto and Karin had already mastered it. It made sense, seeing as their father invented it.
But still, it was beginning to look like no matter how many times Shinji's tried it with clones, it wouldn't work.
His clones kept landing inside of walls and buildings all over the village except for the one place he was trying to go. The Hokage Tower office.
Right now, Shinji was out in a training field by a lake when, from behind him, Misato walked up who's outfit now had a Leaf headband around her waist, using it as a belt.
Misato looked at Shinji, her one-time charge, but now that they were the same age, they had become boyfriend and girlfriend.
Everything that had happened was so crazy. They still had no idea how Shinji had the Sharingan.
Misato watched as Shinji fell to his knees as he panted. He had finally reached his limits, something Misato never thought that she would see.
Misato ran to him and called his name as he fell backwards on to his back.
Shinji looked up to see Misato hanging over him. He panted out, "Relax, Misato. I'm just wiped out."
Misato smiled as she laid Shinji's head on her lap. "Shinji, you've always worked so hard for everyone else. First, it was for NERV. Then, it was the Leaf. Now, it's to save a world. I can't believe I said that last one."
Shinji relaxed as he got some memories from his clones, still wildly transporting around the village. "I know. Life can be so weird. Well, I'm out of chakra. I hope my clones get the hang of this soon."
One of Shinji's friends' teleported in on the woman's hot springs and quickly dispelled. Shinji was going to have to be on guard for angry lady ninja for a while.
Another clone finally landed in the Hokage Tower office which made Tsunade spit her sake out all over the clone from the shock. The clone dispelled.
Shinji smiled up at Tsunade. "My clones are getting the hang of it."
After a while, the last of the clones all made it to Tsunade's office. Thankfully, the shock had worn off and Tsunade paid no mind to the clones popping into her office before turning into smoke clouds.
That night, while Shinji laid in his bed, he thought to himself, 'I'll be coming for you soon, Gendo.'
To be continued next chapter. To NERV.