The story picks up after The Second Raid as Amalgam's fight against Mithril heats up.
Kaname’s a popular girl at her high school, but it’s her popularity off campus that’s the problem. Unbeknownst to Kaname, terrorists are plotting her abduction, believing she possesses the abilities of the “Whispered.” That’s where Sousuke enters the picture. He’s a soldier from Mithril, a secret counter-terrorist unit—and he’s going undercover at Kaname’s school to try and keep her safe.
Summary taken from: MyAnimeList