Three years after the good ending of A Different Path, Emiya Shirou lives a relatively peaceful life running random tasks for Rin in her experiments with the Second Magic while trying to get a better grasp on his own Magic. One day, returning to Japan from a trip overseas, he finds out that Tokyo has been bought out and his parents are alive. Weird how that works out sometimes.

It's back to Alaska for the 37th CMB. The near disaster caused by the 'Mirror of Truth' is sending shock-waves through the Legitimate Kingdom, with Baby-Magnum's pilot at the center of it. The Battalion has always picked itself up and carried on, but when new orders come down the core team will have to do without one of their most important members.

Roxas has been given a chance to exist in Sainan Town. Now filled with a new purpose and living a with an alien nurse named Ryoko Mikado as his adopted mother he become his own person. As Roxas learns about becoming a person, he also rescues a runaway alien princess. However, as a keyblade wielder he also must protect his new home from otherworldly dangers.