Scott Pollert wrote:

SPOILER ALERT
Don't advance if you haven't seen EoE!
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[snip explanation of why Yui went into unit 01]

So, Yui's 'death' is NOT Gendo's fault. Everything else that happens
afterwards is, but really, the one responsible for starting the whole mess
is Yui herself, with a little help from Fuyutsuki.

True, but the question you have to ask now is "Would Yui tell Shinji 
that?"

Considering all that Yui and Gendo have done to advance their own 
agendas - well, mostly Gendo, but Yui as well to a lesser extent - it 
wouldn't surprise me if Yui intentionally didn't tell Shinji about 
her willingly going into unit 01 and *knowing* that she was going to 
be absorbed. After all, Shinji was too young to remember much of 
anything from that time except what he saw, and Gendo didn't fully 
know what Yui was up to, so the only person who could've set Shinji 
straight about the truth was the one person who (in this fic, at  
least) had a vested interest in Shinji *not* knowing the whole truth.

Remember, just because someone says it, it doesn't mean it's the 
truth. And if someone *doesn't* say it, it doesn't mean that *that's* 
not the truth, either.


Derek