During a battle with Shredder, Michelangelo, his brothers, Splinter, Shredder and a large number of Foot Ninja were all transported to a different dimension. When Shredder kidnapped Dr. Naveen Khan and began stealing equipment to build a portal between worlds, Michelangelo and his brothers attempted to stop them.
These attempts brought them to the attention of Batman, who soon found and fought the Turtles. Michelangelo crashed into a pizzeria and loudly warned the people there, before Batman dragged him back out into the street and defeated him. Afterwards, Michelangelo began charting Batman's characteristics as "awesome" and "not awesome," and offered Raphael a "pizza hug" as consolation for losing his sai.
Michelangelo followed his father to the Bat-Cave, learning on the way there that the dimension itself was causing the mutagen in their bodies to become inert. Despite this dire prospect, Michelangelo was delighted by the Batcave and pretended to ride on the back of Batman's robot Tyrannosaurus Rex. Batman became sympathetic upon listening to Splinter's description of their plight and their enemies, and promised to get them home that very night. Unfortunately, Shredder destroyed Dr. Khan and the dimensional portal to keep his mortal foes from being able to return home.
Now staying in the Wayne mansion, Michelangelo became a source of frustration to Alfred Pennyworth because of his pizza consumption and tendency to skateboard indoors. He also convinced Batman to eat a slice of pizza, shortly before Raphael stormed out of the building. When an alert sounded, Michelangelo accompanied Leonardo and Donatello to Casey Jones, shortly after Shredder and Ra's al Ghul had taken five canisters of mutagen from him.
Michelangelo then returned to the Bat-Cave and began playing video games on the Bat-Computer, but was interrupted by the arrival of Robin, who presumed he was an intruder and thief. When it was revealed that Casey had a way home for the family, Michelangelo expressed sorrow that it was over, and hugged Batman.
When Batman was captured and threatened by a number of newly-mutated enemies, he and his brothers chose to save the superhero rather than going back to their own world. Michelangelo in particular fought Mr. Freeze, whom he was delighted by. He then joined his brothers in defeating Ra's al Ghul, eventually triumphing over the man. After their victory was assured, April O'Neil and Casey appeared, having risked their lives to open a portal to Batman's world. Michelangelo and his family returned to their own dimension.
After the imprisonment of the Shredder, Michelangelo and his brothers tried to deal with the internal strife of the fracturing Foot Clan. He rescued Oroku Karai when she was thrown off a train, but the Turtles quickly had to retreat when one of the Foot Elite nearly killed Donatello.
After Bane appeared in New York, Michelangelo joined Raphael and Leonardo in trying to stop the chaos, while believing that Donatello had been kidnapped by the Foot Clan. When Donatello returned with Batman and Robin, Michelangelo was overjoyed by the reunion with the superhero.
He then spent the rest of the day playing video games with Robin, but this led to friction between Robin and Raphael. When the two began fighting, Michelangelo was one of the spectators, becoming alarmed when the fight became too intense. He then accompanied his family in an attempt to take out Bane that evening. It turned out to be a trap, and the group were offered a chance to kneel before Bane and serve him. In the resulting fight, Splinter was badly wounded, and Michelangelo's efforts to raise the spirits of the others was fruitless.
In the following days, the near-death of Splinter and the loss of a Venom-crazed Donatello weighed heavily on Michelangelo, who sought reassurance from April. He was shocked when Donatello returned, with his size and musculature enhanced by the Venom in his system.
He, his brothers, Nightwing, Batgirl and Robin were all brought to Liberty Island in the Turtle Van, and catapulted into the midst of the newly de-Venomed Foot Clan. Michelangelo fought continuously until the Shredder arrived and disrupted Bane's power. After that, he fought Rocksteady and Bebop before being briefly knocked back by Bane. Upon Bane's defeat by Donatello, the Turtles were victorious.
Before the Bat-family's departure, Michelangelo posed for a group photo with his friends and family.