Rei II Chooses Shinji Over Gendo
SPOILER!
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Rei begins the series defined by obedience and by a bond with Gendo that Shinji does not understand.
Across the middle of the series, her relationship with Shinji becomes increasingly personal. By the time
Armisael attacks, her willingness to destroy herself to protect him is not the behavior of a disposable tool.
What changed
Rei's choices begin to come from relationships she formed herself rather than from the role
NERV assigned her.
The Replacement Rei Exposes Gendo's Blind Spot
SPOILER!
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After
Rei II dies, Rei III returns in a familiar body but does not reproduce the exact emotional relationship Gendo expects.
Gendo has built an entire plan around the assumption that Rei can remain a controllable vessel.
Why it matters
The replacement system can reproduce a body. It cannot guarantee the same person will keep making the same choices.