Pepperoni is a female protoceraptops that Raphael encountered during the events of Teenage Mutant Ninja Turtles: Turtles in Time, when turtles were trapped in the Cretaceous by the Utroms. Raphael is captured by the aliens and locked in the same cell with Pepperoni, who receives her name and a ninja bandana from Raphael herself. Leonardo, Michelangelo, and Donatello rescue both from their hole and all together flee from the Utroms. After these events, and while the Turtles and Pepperoni rest, the former are taken to another time, leaving the baby dinosaur behind.
Later, during TMNT: Bebop & Rocksteady Destroy Everything!, she reappears again when the Turtles search for some time-lost Bebop and Rocksteady. Because of this, they travel back to the Cretaceous and are reunited with Pepperoni, who recognizes them and jumps into Raphael's arms as a show of sympathy, friendship and affection. Then Pepperoni jumps with them through a time portal to pursue the two thugs, but in the course of the journey, the little dinosaur wanders off and gets lost without knowing where she has gone. The Turtles travel to Stockgen in 2012 to stop their enemies and there, while a great battle unfolds, Pepperoni reappears in the middle of it and is picked up again by Raphael. Soon after, she is the one who gets the temporary key that allows to stop Bebop and Rocksteady, allowing the Turtles to return everything to normal. Since that time, she is in the present day living as a member of the Turtle family and serving as Raphael's pet.