A high-school-age boy named Yoshichika Tsurugi, who was formerly an ALCA Logicalist until he lost his Logic, finds himself caught between protecting his family as a civilian from otherworldly incursions and rejoining ALCA when his Logic is found.

Yoshichika is obliged to go through a two-day trial period to be reinstated to ALCA, during which he excels at his tests and manages to step on his team leader's toes. Yoshichika meets Olga, and is curious about the special treatment he receives.

After Tamaki is replaced as team leader by Yoshichika, she is devastated. Yoshichika learns from Veronica about how he and Tamaki are not that much different in their respect for life. Veronica must take combat matters into her own hands.

Chloe becomes occupied with investigating the Paradox Level 9.8 readings that previously appeared, stepping on the toes of the designated research staff. Chloe disobeys orders to tackle a Foreigner on her own.

Yoshichika and Yukari discover that Mana was abandoned as a child, and that even now, she hopes to contact her parents again. When a Foreigner shows up that proves too difficult for Chloe and Tamaki to handle, Mana makes a stunning decision.

Yukari dreams of doing more as a Logicalist, but her lack of experience and inability to Trance with any of the others during training sessions holds her back. A crisis in the Foreigner holding facility threatens the entire branch.