Michelangelo was told that Pete's injured wing had fully healed, and rather sadly released his little pigeon friend back into the wild. However, when the other Turtles were kidnapped, Michelangelo found that Pete was the only witness to what happened, and was told about what occurred by him.
Pete accompanied his Turtle friend throughout his infiltration of Dr. Lesseau's secret facility, where he demonstrated their unusual bond several times. He also helped stop Lesseau by putting leaves and dirt over the man's surveillance cameras.
Pete seemed to be able to communicate with Michelangelo through pigeon coos, and was unusually intelligent for a pigeon. In turn, Michelangelo was highly defensive when people doubted Pete's intelligence and communication abilities.