The Baroness is recovering from her brainwashing she had during her time in Cobra with the assistance of Destro and Scalpel. General Joseph "Joe" Colton comes back to fill in for Hawk as commander of GI Joe. Destro consolidates his power with the Cobra organization. Clutch, Snakes-Eyes, Roadblock, and Mayday go to the town of New Moon Colorado, to extract Mirage and group of Joe trainees. These trainees include a new guy named Thomas Stall.