T · B from Ikari. The shadow created by the scaffolding is forming a cross.
IKARI:“That's right.
The path to godhood that none have ever succeeded in before.
The Human Instrumentality Project.”
Editor's Note: Translator notes that this scene is inherently highly ambiguous and that Gendo's original Japanese phrase kami e no michi (rendered here as "path to godhood") leaves a lot of room for interpretation.
Dr. Nick: Notice what's not happening in this scene: Fuyutsuki stays steadfastly with team Yui and doesn't reveal her plans to Gendo even when he seems to be going truly off the deep end now. (Continued in additional comments)
Additional Commentary
Dr. Nick: (Continued from previous comments) Now, Gendo is a smart guy, and he figures out what Yui is planning to do by letting herself be absorbed in the Eva. Perhaps the realization set in after the salvage attempt failed - Yui wants to stay in the core. Knowing this, he's not surprised or shocked whenever Unit-01 takes independentaction. In effect, Gendo's Human Instrumentality Project plan just builds a selfishly motivated extra conspiracy on top of Yui's conspiracy within Seele's conspiracy (whew!): if successful, Seele's ultimate goal is thwarted like Yui wanted, but the Instrumentality process allows Gendo to slip in and be with Yui like he wanted.
Here too there are of course some extra mysteries. For example, Gendo susses out Yui's motives, but does he stay unaware of Fuyutsuki's position as Yui's co-conspirator? I would assume so, as I doubt Gendo would be particularly merciful towards a person who, by inaction, allowed Yui to be ripped away from him. And did Yui foresee how losing her would change Gendo as a person? Did she count on him crafting his own extra conspiracy to run parallel with hers, helping hers along? That is the sort of masterminding that brings us right back to sociopath Yui.
UrsusArctos: The entire lack of communication between Yui and Gendo, or any post-transformation attempt at letting Gendo know what she had in mind is probably one of the biggest mysteries in the show and it really does paint her character in a very poor light. If she'd known that she'd made Gendo dependent on her emotionally and caused him to start seeking her obsessively - without any real care for the damage it caused him or Shinji - it'd be hard to consider her anything other than a sociopath.
Speaking of light, the shadow of the cross should fall on Gendo, although it doesn't, making it look like Gendo is carrying the cross of the burden he's about to bear. Symbolically this image is as ominous as it is deeply tragic, and when the "sociopath Yui" angle is added it just becomes worse, with Gendo being symbolically crucified as a victim of Yui's motivations. Gendo may have been firmly on the side of the villains, but it's hard not to feel bad for him here.
