Contains spoilers for this episode and earlier episodes.
Unit-01's defeat of the Angel leaves Nerv facing a machine that has escaped its restraints and a pilot who cannot be recovered normally. Shinji's synchronization reached a level that dissolved his body into the entry plug's fluid. His components remain present, but he no longer has a separate physical form. Misato demands that Ritsuko take responsibility for bringing him back, while the committee questions Gendo over the Eva's transformation. Ritsuko prepares a salvage procedure intended to reconstruct Shinji's body and return his consciousness to it. As the days pass, Unit-01 remains immobilized in its cage and the people outside can only work toward another attempt.
Inside the Eva, Shinji moves through memories, accusations and imagined conversations about his father and his reasons for piloting. He connects the kindness he receives to his usefulness in battle, unable to imagine what value he might have otherwise. The salvage operation fails to bring him out, and the entry plug releases his suit without his body. Misato breaks down beside it. Shinji then encounters the presence of his mother and a memory of his parents discussing their child. He returns physically from Unit-01, allowing Misato to hold him again. Later, her renewed relationship with Kaji also becomes an exchange of secrets when he gives her information gathered during his investigation.