Practice runs for the new railgun, Mega Shot, are conducted in Anri's hometown. That's where Anri has an unexpected reunion with her childhood friend, Mizuho.

Mizuho begs for them to cancel the practice runs. She insists that the removal of the shrine for the installation of the Mega Shot will awaken Dorgo, the local guardian god, but Anri finds it hard to believe.

However, during the practice there's a big earth tremor...

As the network contamination by Gebalga continues to spread, SKaRD plans a new operation. Gento is distrustful of Blazar, who has once again acted against his will in the battle against Gebalga. He decides to leave the Blazar Stone in his locker. SKaRD decides to commence a major joint-operation by combining forces with the development team and the special forces unit.