There is no true fact or answer to this question...they are all just theories and speculations.
Theories
I heard from somewhere that someone thought the reason for Unit-00 going berzerk was
because Dr. Akagi was dissolved into Unit-00...uh. Maybe. But it doesn't make sense because she killed herself.
But, Dr. Akagi did hate Rei..er Yui...er whatever. Maybe she was popped in there after she died...heck I dunno.
My Theory. Her only link is the fact that she's an angel. Which kinda explains why Unit-00 goes
nuts, instinctive aggressive urges? So this kinda makes her compatible with all the other Eva's, she was able to synch with
Unit-01, heck her dummy plug did also. But honestly I really don't know why Unit-00 went crazy, I mean it did
with Shinji also...Hell I really don't have a strong backing on this one I have to think about it...someone help me.
ok what I really think...Rei is an Angel, EVA's destroy Angels, Angel inside EVA, EVA tries to kill itself...make sense? I know it's vague but that's the best reasoning I can do right now.
Reader Theories:
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For Rei's link to EVA-00/why EVA-00 went crazy. I heard/saw
that Ritsuko privatly thought that EVA-00 went crazy because
it was trying to kill her. This was explained as Rei's
subconsiously hating Ritsuko, therefore when Rei provided a
soul for EVA-00 her hatred for Ritsuko went with it. Thus,
when it went berserk it punched the window to the control
room. In addition, in i think episode 5 or 6 the episode
where Ritsuko talked about the EVA-00 going berserk she said
that the EVA-00 might have went out of control because of...
she became silent and thoughtful.
-ShiniKami
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About Eva 00 attacking Gendo and Ritsuko (as well as Asuka
"finding' her mother in Eva 02.) I think that piloting an
Eva leaves a "ghost" impression of the soul of the pilot.
This ghost cannot activate the Eva (like the complete soul
of Yui can Unit 01) but can influance it. If Ritsuko's
mother did pilot unit 00, the residual soul could retain
her jelousy for Gendo (especially if it knew what was going
on between Gendo and Ritsuko.)
This would also explain how Asuka recognized her mother
in Unit 02, even though her mother was not dissolved like
Yui. (Also, remember, it was piloting Unit 02 that drove
Asuka's mom nuts. Maybe the rational part of her mind
bonded to the Eva. Just a thought.
-James M. Gill