Stockman becomes one of the main antagonists of the fourth season, with Bishop, Hun, and Karai. Stockman helps engineer a faux alien invasion to convince the White House to continue funding the EPF, but this backfires disastrously when left-over fluids from the deceased cloned aliens begin to mutate the animals and people of New York, sparking an outbreak. After transferring Bishop into a new body, Stockman briefs Bishop on the situation and is deployed to New York to try to contain it. The outbreak proves too much for both the EPF and the Turtles to handle, however.