This is just a weird idea i had for a one-shot, it came to me about an hour ago and i figured it would be funny.
Here is the real reason that unit-00 went berserk when Shinji was sitting in it for the cross activation experiment.
So, without further Ado, i bring you...
Neon Genesis Evangelion: The Itch.
Unit-00 was locked into the cage and restrained quite securely.
After the berserking incident during the cross activation experiment Dr. Akagi had decided that no chances could be taken, and so she had the unit put on complete lockdown until a solution to the problem could be found. It just wouldn't do to have such an un-predictable Evangelion unit.
Lt. Maya Ibuki was discussing the situation with her superior, one Ritsuko Akagi. She held her clipboard to her chest and spoke, "I'm sorry, I've been looking and looking and I can't find anything in the computer logs that would explain this incident. Have you found anything?"
The bottle blonde doctor shook her head, "Not a thing, its probably just mental instability in the pilot. We'll have to work on filtering out thought noise; that should fix the problem."
"If you say so."
The two women took one more look at the cycloptic head of Unit-00 and left the cage. The lights dimmed and then finally shut down completely as the sensors detected a compete lack of movement in the cage.
The single eye of Unit-00 glowed briefly and an androgynous voice came from the Unit, "If you had to wear this armor all day you'd go nuts too. So…itchy."
The Eva moved in its restraints, trying to scratch the itch.
In the main control room alarms went off. Aoba turned around to Misato, who had been passing through to pick up a report from the bridge crew. He shouted in a panicked voice, "Seismic activity detected originating in cage seven!"
Misato paled, "An Angel!?"
Aoba looked back at his screens and then back to Misato, "er…no?"
In cage seven Unit-00 sighed, "That's so much better…"