It's back-to-school mayhem with Kaname Chidori and her war-freak classmate Sousuke Sagara as they encounter more misadventures in and out of Jindai High School. But when Kaname gets into some serious trouble, Sousuke takes the guise of Bonta-kun - the gun-wielding, butt-kicking mascot. And while he struggles to continue living as a normal teenager, Sousuke also has to deal with protecting his superior officer Teletha Testarossa, who has decided to take a vacation from Mithril and spend a couple of weeks as his and Kaname's classmate.

Three months after the original series Mithril learns of a secret organization that has technology able to counter the ECS (Electronic Conceal System) mode. The organization, known as Amalgam, has access to Black Technology, which was obtained from the Whispered. Like the other intelligence agencies, Amalgam intends to obtain more. Sousuke's mission to protect Chidori is terminated by Mithril, instead leaving her in the care of an anonymous agent known as Wraith.

Sousuke Sagara, a member of a covert anti-terrorist private military organization known as Mithril, tasked with protecting Kaname Chidori, a spirited Japanese high school girl.