The Ninja Turtles encounter them while out looking for April, and during the fight, they combine into one giant mutant. Raphael smashes them back apart with his tonfa, and they are all beaten by the Turtles and April, save for a few who end up chased by a crossing guard.
They appeared in the museum in "Stuck on You", where the Turtles found them eating the art exhibits. After the arrival of Hypno-Potamus and the Foot Clan, the Turtles first attacked the Silverfish. After some initial difficulties, the Turtles successfully defeated the Silverfish and dropped them in a trash can.
The primary power of the Mutant Silverfish is the ability to duplicate themselves when they sustain any sort of strong impact. They can also combine themselves into one being.