The Shogun and her escorts have been surrounded by the rebels, who have offered them a 60 minute ceasefire in the hopes of a peaceful resolution. Can Takeru, the 207th Training Flight, the Royal Guard, and the US Army find a way past them to return to Yokohama Base?

As Takeru and the 207th Training Flight escort the Shogun across Japan, Professor Yuuko's personal task force fights a desperate battle to keep the rebels off their tails.

Takeru and his training squad head out to assist the UN and Japanese forces in dealing with a coup d'état, but they find themselves dealing with what might be the most vital mission in the entire conflict.

An insurrection threatens to ignite a full-scale civil war in Japan, and the 207th Tactical Armored Flight finds their first combat mission might be against other humans, instead of the invading BETA aliens.

Takeru's trip back to his original world concludes after an encounter with his childhood friend, Sumika. After his return, he learns about the enigmatic Yashiro Kasumi's mysterious past.

In order to help Professor Kouzuki fulfil her plans for Alternative IV, Takeru partakes in an experiment designed to send him back to his home world.

Takeru and Professor Kouzuki have collaborated to create a new operating system for the 207th's Tactical Surface Fighters, making the anti-BETA weapons more maneuverable and responsive than ever. But will it even matter if Yuuko can't actually make some progress on the mysterious Alternative IV plan?

Takeru's efforts to change the future are starting to have an effect, as the 207th's Tactical Surface Fighters show up earlier than in the previous timeline. And if an idea he's cooking up works, it might make them even more effective weapons against the BETA.

As Takeru starts to feel anxious about whether or not he can actually make a difference, Professor Kouzuki demands more concrete evidence of his knowledge about future events.