Following the issues that Miharu Oozora had with her Comet Blasters, the Cosmic Emergency Management Agency (CEMA) realizes it can no longer completely rely on human pilots for interception missions. Instead, an old program with unmanned shuttlecraft is revived for trials. Meanwhile, back on Shimoji Island, Mikaze and her friends finally take their pilot licensing test as the next batch of rookies arrives at the base.

Things quickly heat up when one of the orbital bases nearly breaks down, forcing an impromptu rescue mission. With CEMA tearing itself apart over how to handle the crisis, the larger mystery surrounding the comets begins to unravel.