Contains spoilers for this episode and earlier episodes.
After killing Kaworu, Shinji cannot settle the guilt by telling himself that he had no alternative. The question of why he pilots returns, and familiar voices challenge his claim that he acts only for humanity. Asuka accuses him of seeking approval and depending on the happiness others give him. The questioning turns toward her own dependence on being an Eva pilot, while Rei confronts the problem of several bodies bearing the same identity. Their fears are presented through inner conversations rather than another military confrontation. Gendo calls Rei to accompany him, and Human Instrumentality brings the characters' divided perceptions and unmet needs into contact.
Misato's memories expose the obedient child who hoped to keep her family together and the adult who sought closeness while fearing what it revealed. Her relationship with Kaji becomes part of an examination of grief, desire and self-disgust. Asuka revisits her mother's rejection and her insistence that she would never need anyone, yet cannot suppress the wish to be protected. Shinji likewise wants other people to remain with him while resisting the pain they can cause. The questioning gathers around a stage and audience, where different versions of him face one another. He is confronted with the possibility that his isolated world answers his own wish to avoid being hurt.