Contains spoilers for this episode and earlier episodes.
Ritsuko finishes routine work on the Magi supercomputers before a new synchronization experiment places the pilots in simulation bodies. What looks like corrosion in the testing chamber begins spreading rapidly, and attempts to contain it fail. Rei's simulation body moves violently, forcing the staff to eject the pilots. The contamination then produces an A.T. Field, identifying it as an Angel rather than an ordinary technical fault. Gendo orders the Evas sent away without their pilots to protect them from infection. Ritsuko and Misato must fight the intruder through the base's environmental controls and computers instead of relying on the machines normally used against Angels.
An oxygen attack briefly appears promising, but the organism adapts and starts building electronic circuits. It takes over one Magi component and pushes for headquarters to destroy itself, then attacks the remaining computers to secure the necessary agreement. A temporary barrier gives Ritsuko time to enter Casper and prepare a response using her mother's notes. She exploits the Angel's capacity to evolve, directing that process toward its own extinction before the last computer falls. Nerv survives with moments remaining. Afterwards, Ritsuko explains that Naoko Akagi built the three Magi personalities from herself as scientist, mother and woman. The rescue leaves Ritsuko reflecting on her conflicted feelings about those different sides of her mother.