Following the events of Trails from Zero, the Special Support Section find themselves with new members and new duties. However, rising tensions in Crossbell along with pressure from two neighboring political powers threaten both the safety of their home, as well as the integrity of their team.

Set just a few months after the events of Trails from Zero, a temporary peace has settled over Crossbell and the Special Support Section find themselves with newfound fame and status, thanks to their heroic actions.

However, the peace is soon broken with the rise of multiple organizations with ulterior motives. Framing these growing tensions is the increasing pressure from the Erebonian Empire and the Republic of Calvard, with Crossbell caught between them. With the safety of their home and the foundations of their team now on the line, Lloyd and his allies must gear themselves for the threats that loom ahead. Little do they know that Crossbell will soon become the stage for a climactic conflict that will determine its future...