By the time of the second season, Stockman was recovered and forced back into the Shredder's service, though now the Shredder has the power to torture him whenever he steps out of line. Stockman is able to trap the Turtles inside the Utroms' virtual reality, and when they do emerge, confronts them with the rest of the Foot. Professor Honeycutt later inadvertently frees Stockman from the Shredder's control, and Stockman gleefully turns on his master and subdues him, leaving the Foot. After the Shredder's apparent death, Stockman began working for Leatherhead, helping him to build a transmat to journey to the Utroms' homeworld. Stockman's deception is unveiled by the Turtles, and the scientist flees, but not before causing Leatherhead to become trapped in a cave-in. Stockman later aligns himself with the mafia against the Foot and the Purple Dragons during the turf war in the wake of the power vacuum left by the Shredder's defeat.