Michelangelo is a member of the Ninja Turtles, along with Leonardo, Raphael, and Donatello. Along with his brothers, he was raised and trained by his father Splinter, and resides in the sewers of New York City. He is considered the most playful and energetic of the four brothers, and has the greatest love of pizza.
When Shredder made an alliance with an unknown person in Gotham City, Michelangelo and his brothers headed there to stop their mortal enemy. They attempted to thwart the theft of several pieces of technology from various corporate laboratories, but were unsuccessful. When they attempted to stop the Foot Clan from stealing a cloud-seeder from Wayne Enterprises, they instead ended up fighting the Penguin and his men. Despite being their enemy, Michelangelo was delighted by the Penguin's odd weaponry, and found Gotham to be a "bonkers" place overall.
Their efforts brought them to the attention of Batman, whom Raphael recklessly charged at, sparking off a fight between all four Turtles and the superhero. Michelangelo is thrown into a nearby pizza parlor, where his appearance caused mass panic, before being dragged out again and fighting Batman.
The Turtles later made their way into the Batcave, where an overjoyed Michelangelo donned a spare cape and cowl of Batman's and sat atop the giant animatronic Tyrannosaurus Rex kept in the Batcave. He was then attacked by Robin, sparking a fight between the boy and the four Turtles, and eventually had to lie on top of Robin to immobilize him. Batman then returned, and was told by the Turtles about their common enemy.
Michelangelo quickly became a nuisance to Alfred Pennyworth, with his skateboarding inside Wayne Mansion and his messy consumption of pizza. He also attempted to coax Batman into trying a slice of pizza, and was baffled and mildly upset when the superhero rejected it.
Upon hearing of the Arkham Asylum inmates taking over the facility, Michelangelo and his brothers accompanied Batman there, and found that the inmates had been mutated. Raphael, Michelangelo and Robin ran afoul of Mr. Freeze, now a mutant polar bear with an ice gun, which delighted Michelangelo, and eventually managed to escape him. They then encountered Poison Ivy, now a mutant plant, but were able to elude her when her roots kept her from reaching them.
When they reached the Joker, Harley Quinn and Two Face, Michelangelo and Robin joined forces to try to stop Mr. Freeze. They were unsuccessful, and could only watch as the Joker transformed Batman into a crazed mutant bat. Michelangelo joined his brothers in trying to restrain Batman, and was later thrown the retromutagen as Batman carried him off. He was able to jump onto the deranged mutant's back and inject him with retromutagen, reverting him back to his human form.
While Batman was unconscious, Michelangelo was shocked to discover that he was actually Bruce Wayne, something his brothers had figured out long ago. When a recovered Batman voiced his intention of stopping his enemies without the Turtles, Michelangelo protested at first, and seemed saddened by the prospect. Fortunately, Raphael convinced Batman to give them another chance, and Michelangelo excitedly declared that he was going to ride in the Batmobile.
While in the Batmobile, Batman sternly told Michelangelo not to press any of the tempting buttons in the car. However, he changed his mind when the Batmobile was immobilized by a large number of ninja, ordering the ecstatic Turtle to press buttons. Michelangelo complied, pressing every one available until forced to stop and complimented by Batman.
When they reached the Ace Chemicals facility, Michelangelo joined his brothers in fighting the combined forces of the Foot and the League of Assassins. He spotted Donatello clinging to the rising mutagen-disseminating device and hopped on as well, where his efforts to turn it off caused the opposite effect. Eventually, he was able to damage it, and his continued efforts to do so led to the machine exploding and plummeting out of the sky. Donatello and Michelangelo fell as well, but landed safely on a passing blimp.
Upon returning to the Batcave, Michelangelo apologized to Alfred for his prior bad behavior, and gave the butler his skateboard as a gesture of repentance. He was delighted when Batman revealed some newly-delivered pizza, carrying Alfred over to the food before eagerly partaking.