The game takes place at the same time frame as Zero and Ao no Kiseki in the Erebonian Empire. The game’s plot is centered around the newly formed special class “Class VII” in Thors Military Academy, composed of both aristocrats and normal Erebonian citizens.

Trails of Cold Steel II begins a month after the end of Trails of Cold Steel, with Rean having escaped with Valimar. He makes it to his hometown of Ymir where princess Alfin also escaped to, but she is kidnapped along with Rean’s sister Elise. The rest of class VII has scattered over the country and he goes around gathering them and other Thors students, and after being given the airship Courageous by Olivier, uses Valimar to help civilians and look for Alfin and Elise.