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I was always confused as to why unit 01 was crucified and it was Shinjis choice to accept or reject instrumentality, why was unit 01 the catalyst for this event
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I still don't fully understand everything, but I'll do my best to fill you in on what I do know. In 2004, Yui Ikari, Gendo's wife and Shinji's mother, participated in a 'contact experiment' with the core of the still unfinished Unit 01. The way the experiment was carried out was the exact same procedure taken on Adam at the South Pole, which caused the Second Impact. Upon coming into contact with the core (we still don't know what this means, Gendo ran his hand over Shamshel's shattered core in one of the early episodes with no problems), Yui's soul was sucked from her body into the core, where she chose to remain in order to initiate Third Impact.
When Unit 01 fully awakened following Asuka's death (the awakening is what allowed her to break through the bakelite and let Shinji enter), Yui became completely conscious. Whereas before, she only had a vague idea of what was happening outside of the Core and the Entry Plug, now she was fully aware. Using her AT field (I think), she caused the Lance of Longinus to rocket back from the moon, because it was the only weapon that can penetrate AT fields, and allow humanity to revert to LCL. Using this weapon in conjunction with the insanely powerful AT field of a loving mother, combined with the AT field of a boy who has completely lost his mind, the Lance allowed Unit 01 to transform into the Tree of Life. The only reason I can see that she was crucified was to help the Eva Series lift her above the clouds and hold her there.
Shinji remained in charge of Instrumentality because he was technically the one that made it happen. Third Impact didn't necessarily have to take on the form of Instrumentality, but that was Shinji's wish; to rid the world of pain and suffering, make us all one. Things go well (as well as things can go when everyone is bursting into orange Gatorade and their souls are sucked into a giant 14 year old's head) until Shinji realizes that Instrumentality is just another form of running away. He had established earlier in the series that running away from your problems solves nothing, and he understands that the feeling of happiness and completeness he feels in Instrumentality is fake. When everyone is one, nobody really feels anything. Shinji knows that happiness can't last forever, and that one day, all he currently knows will be gone, but he also comes to understand that sadness isn't eternal either, and that when people are individuals, their feelings are real. Shinji rejects Instrumentality, and Lilith's body falls apart, releasing all the souls of the Earth, even those of people who had died before Third Impact. Gendo likely stays in the Core of Unit 01 to be with Yui forever, although this is never confirmed. Anyone who wants to come back can rematerialize from the sea of LCL, Shinji and Asuka just happened to be the first ones to do so on that particular beach.
I've reached a point where I just generally don't give a fuck anymore. In a good way.
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Because Gendo made the Spear of Longinus irretrievable, Seele were forced to use Eva-01 for their plans instead. Eva-01 was to be the yorishiro -- the vessel for the complemented souls of humanity. In being "crucified", Eva-01's Doors of Guf were forcefully opened, and made ready to receive souls and direct them into the Chamber of Guf. Had Lilith never intervened, the Anti A.T. Field created by the ten Evas would have probably done the trick on its own, and the MP Evas would have directed all of the souls into Eva-01 and the Black Moon.
The reason why Eva-01 and the Spear fuse to create the Tree of Life likely has something to do with enabling Instrumentality. Going by Kabbalistic precedent, the Tree is a sort of linking element between physical and spiritual reality, or between Man and God. Effectively, a conduit by which souls can become as one again (a state called Adam Kadmon) and exist in a place close to God.
and it was Shinjis choice to accept or reject instrumentality
It was Shinji's choice because Yui, Rei, and Kaworu all decided that he should have it. On the more technical side of thing, there is some possibility that a Seed of Life needs to receive the "okay" from a representative of descendant humanity in order for any changes to be made to an established biosphere. That is to say, once a planet has been colonized, what's been created cannot be annihilated willy-nilly; a failsafe is in place. I suspect this because all of the biosphere-altering Impacts (including potential ones) we know about involve a member of Lilin- or Angel-kind effectively "triggering" a Seed into Impact Mode. This includes Second Impact: Adam is awakened via contact with a Lilin, resulting in Adam's attempt to reclaim Earth from Lilith.
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