After being sent to Tokyo, the Aragami-target Momoji discovers that she is now under the care of the TAC. She knows these monsters are terrible, evil things, and really wants to help, but can't find out how to.

The TAC soon discover that their base isn't as safe as they thought when an Aragami breaks in and attacks.

Kusanagi is outraged when Mrs. Matsu-Daira sees Momiji as a live specimen, free to experiment on her. Just as Momiji is about to confront Kusanagi on the threat he made to the lady and her son, a strange jellyfish emerges from Tokyo Bay and things heat up.