Fifty years after the Mutagen Bomb detonation, Chompy has grown significantly and was taken care of by Michelangelo. He was shown to be the guardian of the Holy Chalupa's home and attacked Raphael, Donbot and Mira. Michelangelo stopped Chompy from devouring Raph and told Chompy to look at Raphael, Chompy instantly recognizes Raphael as his father and playfully bites him.
Now that the family is partially reunited, The Turtles and Mira hitch a ride on Chompy to their home, the last building standing in the wasteland. Chompy is then forced to stay outside and rest because he can't fit inside. He is then seen roaring repeatedly as he watches Mira being taken by the Honey Badger Ravagers and Scale Tail Clan, When Raphael dodged an incoming rocket, he realizes it was heading for the restaurant. The building blows up with everyone inside and Chompy got caught in the blast.
Chompy resurfaces from the rubble of the collapsed pizza place with seats and a machine gun on top of his shell, and attempts to sniff out Mikey to save him, he is unconscious but the fire turtle then licks him to wake him up, thanking him he goes to save Ice Cream Kitty. Chompy then sniffs out Donbot and picks him up from the destruction. They then go to save Raphael and Mira from Verminator Rex.
Chompy and Michelangelo infiltrate the Scale Tail Fortress by ramming the gates and the lizards guarding the base. After Raphael is declared leader of the Scale Tail Clan and the Honey Badger Ravagers, forming them together as Red Stripe Army, Chompy and everyone begin the road trip to Oasis. But the trip goes off course as Verminator Rex returns with his master Maximus Kong, who is later revealed to be the presumed dead Leonardo. Chompy and the rest of his family then make it to Oasis.
Although Chompy isn't seen using any abilities, he can bite anybody, like Raphael.