Pete was an ordinary pigeon that was mutated by The Kraang into a humanoid form. During his captivity, he came in contact with Kirby O'Neil, April's father and also a prisoner of the Kraang. Kirby O'Neil taught Pete how to speak and had him deliver a message to his daughter April O'Neil in which he wanted to warn her of impending danger.
Under unexplained circumstances, Pete was either released by the Kraang after the experiment or escaped his captivity. Pete stalked April O' Neil for a few days and frightened her with his alleged attack before the turtles ambushed him and tackled him to the ground. After Pete had been captured, he was able to tell them his true intentions, he informs April and the Turtles that the Kraang intend to detonate a mutagen bomb into the city. He then revealed the location of the Kraang base in exchange for a loaf of sourdough bread. He then led the Turtles to the hideout of the Kraang where O'Neil was being held.
Pete is seen as one of the many mutant captives of the Kraang. After all of the mutants are released, he is seen flying out of captivity and into the portal back to the city.
Battle for New York, Part 1
Pete is first seen attacking a Kraangdroid for a piece of bread as he helps the Mighty Mutanimals save the turtles from the Kraang after they rescued two humans the Kraang had found, captured and were preparing to mutate. They then talk and go back to the Mutanimals' lair (unaware that the Kraang were following them). They are then introduced to their benefactor (who is Jack J. Kurtzman who survived the invasion). Jack then reveals what the Kraang are planning and states that they all must work together which results in all of them arguing and fighting. Suddenly the Kraang [along with some Biotroids show up and break in as they begin to attack them all. Jack is shot and injured in the process as he tries to retrieve a disc with the info on it much to everyone (especially Pete's) despair. Leatherhead grabs Jack and everyone retreats back to the turtles' (temporary) lair, Antonio's Pizza-Rama. They then decide to team up and stop the Kraang's plan (which is to launch a giant rocket full of mutagen into the earth and mutate the entire planet). They then show up at the launch site and launch a ground attack on the Kraang which is a perfect distraction for the turtles who use their latest invention the Turtle Blimp. Despite their best efforts, Kraang Subprime (who apparently survived his supposed death in the invasion) manages to launch the rocket. Luckily, Donatello manages to reset the coordinates and sends the rocket to the sun and they all glide to safety. Pete is suddenly shot at Subprime's Irma head which Slash destroys. The Kraang then retreat and the two teams celebrate their victory. They all then head to TCRI to enter Dimension X and save the mutated humans.
Battle for New York, Part 2
Pete alongside the other Mutanimals get into TCRI and break into the room where the portal is located as they fight through the Kraang. They manage to open the portal for the turtles on the outside who enter Dimension X. Suddenly they are ambushed by Mrs. Campbell along with some Irmabots and Biotroids. All in the team are captured (Pete is taken down by some of the Irmabots in the process) and the portal is deactivated which leaves the turtles trapped on the other side. They are all then placed in a glass cage which they manage to escape from with help from Dr. Tyler Rockwell (who uses his telekinetic abilities to help free them). They then begin to attack the Kraang again (this time being the winners) and reopen the portal. They then help teleport the humans back to earth after the turtles de-mutate them all and the turtles themselves shortly afterwards. They then appear alongside the turtles on some rooftops after saving the city (with the humans free, de-mutated and returned, the power restored and finally the Kraang defeated). They all then begin to compliment each other for working together and their plan. They all then celebrate and shout "Booyakasha".
The Mutanimals appear at the Turtles' lair to warn them about Don Vizioso's mutant-hunting plot. When Donnie asked where Pigeon Pete is, they quoted "We don't talk about Pigeon Pete."
Pete and the rest of the Mutanimals are seen attending Hamato Yoshi's funeral, paying their respects to him.
Pete was once one of the millions of pigeons living in New York City. Used in one of the Kraang's mutagen experiments, he was covered in the ooze and mutated into his current form. He possesses a human torso with a giant pigeon head and legs. He seems to have several strange mutagenic blue-green growths all over his body. His arms have large wing feathers that somehow grant him flight. Though he has large sharp talons, he does not seem to be a very good fighter. Starting life as a pigeon, he retains his birdlike shortcomings such as slamming into plate-glass windows. He is also obsessed with bread and seems willing to do anything to get it.