Following his victory over Rez in the Media Dimension, Gex has retired from the public eye and turned to solitude. Two years later, his quiet life is soon turned upside down when one day he was watching television when all of a sudden, it goes blank and Rez's image begins flashing on the screen. Two government agents appear and abduct Gex to their headquarters, in which Gex is interrogated. The agents explain that Rez has returned and they need his help in taking him down again. Gex refuses, saying that he has already saved the world once and that they should try to find someone else. When the agents make a fair negotiation for a huge sum of cash and gadgets, Gex tells them everything. He accepts the mission, to which he leaves the building and is then accosted by a female agent who introduces herself as Agent Xtra and wishes him good luck.

After navigating numerous television channels in the Media Dimension, Gex finally confronts Rez and the two battle once again until Gex drops a huge television set on Rez severely weakening him. In desperation, Rez tells Gex through a television that he is his father. Gex merely turns the television off; whether or not he believes Rez is unknown. In the final scene, Gex shares a hotel room with Nikki from the Pandemonium series.