The members of the Initiative are picking up the pieces after the Skrull invasion. The base is now under the leadership of Gauntlet, who is somewhat surprised to learn that he's the ranking officer left on the base. The Shadow Initiative undergoes an overhaul in its membership, the trainees don't know who to trust or what to expect, and a Skrull plot to ensure their "us or nobody" plans for Earth's ownership goes into action.