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One part, for me anyway, that stuck out was the crucifixion by the Mass-Production EVA Units of EVA Unit 01 in The End of Evangelion. I just can't see the reason why EVA Unit 01 was crucified when Third Impact occurred. What was hoped to be gained by crucifying a mech of all things?

What was the reason for EVA Unit 01's crucifixion? Was it to start Third Impact?

I have not read the manga behind Evangelion, so I know I am missing something.

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It seems to be a necessary part of the ritual they are doing but the exact details of it and how it works are unknown.

SCENE: SEELE monoliths
SEELE 09?:
EVA-01 has been marked with the stigmata (sacred insignia).
All (chanting):
To restore the Tree of Life!
SEELE 01:
Our servants, the Eva series...
(Keel appears) Their existence has all been for this one moment.
(Eva series move to the positions of the Sephroticum and shine in circles around the cross of EVA-01)
Script

A reason for the stigmata could be that GNR/Lilith also has them later on in the movie through which she absorbs the souls. Since EVA-01 is made from the body of Lilith these could possibly be caused by inflicting them on the EVA.
Stigmata

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