Contains spoilers for this episode and earlier episodes.
Shinji achieves the best result in the pilots' latest synchronization test, drawing satisfaction from an accomplishment that angers Asuka. When a striped sphere appears above Tokyo-3, his new confidence carries into the deployment. Asuka challenges him to lead, and he attacks before the others are ready. The sphere vanishes, while a black shape beneath Unit-01 expands and swallows it. Rei and Asuka escape the same trap, but Nerv loses communication with Shinji. Ritsuko determines that the shadow on the ground is the enemy's true body and the floating sphere is its projection. Inside the trapped Eva, Shinji can find neither an exit nor useful information about his surroundings.
With life support running down, Misato seeks a rescue while Ritsuko prepares a bombardment that may recover Unit-01 at the cost of its pilot. Their argument exposes Misato's growing anger over Nerv's willingness to protect the Eva above Shinji. In isolation, Shinji faces questions about why he pilots and how he avoids painful parts of his life. Memories of his parents break through as his strength fails, and a comforting encounter recalls his mother. Before Nerv's attack begins, Unit-01 tears out of the Angel's sphere in a violent eruption, killing it. Misato embraces Shinji when he is recovered. He later awakens in hospital, alive but unsettled by what he experienced.