When Shredder made an alliance with an unknown person in Gotham City, Donatello 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.
Their efforts brought them to the attention of Batman, who easily fought and defeated all four Turtles despite being wounded. Donatello was the one who enabled their escape when he saw Leonardo defeated by Batman, using a smoke bomb to conceal the Turtles' departure.
Donatello researched Batman in an Internet cafe, confirming that Batman was a hero who only pursued criminals. Afterwards, he deduced where the Batcave might be found, and led his brothers through flooded underground tunnels to the hidden location. Donatello was delighted by the sight of the Batcomputer and began researching, concluding that Batman was following the same laboratory break-ins that they had.
However, their time in the Batcave was interrupted by the arrival of Robin, who knocked Donatello down with his own bō. He later bonded with Batgirl as they formulated a retromutagen (or "anti-ooze," as Donatello called it).
Upon hearing of the Arkham Asylum inmates taking over the facility, Leonardo and his brothers accompanied Batman there, and found that the inmates had been mutated. Donatello and Batgirl encountered Bane, who had been mutated into a jaguar, and Donatello was temporarily knocked senseless. After taking out Batgirl, Bane attempted to break his spine the way he once had Batman's, but Donatello's hard shell only damaged Bane's knee, giving the pair the needed opening to knock Bane out.
After this incident, the pair found the humans who were being held hostage by the Arkham mutants. Unfortunately, they arrived too late to save Batman from being mutated by the Joker, and Donatello joined his brothers in trying to restrain the crazed bat mutant. They eventually managed to inject him with the retromutagen, returning him to normal.
While Batman recovered, Donatello conferred with Leonardo and Batgirl about the most likely location for Ra's al Ghul and Shredder to complete their plans. He was able to deduce what the mutagen-disseminating device was for, and the effect it would have on Gotham. Upon waking, Batman declared his intention to stop working with the Turtles, and Donatello seemed sadly resigned, but Raphael intervened and talked Batman into working with the Turtles once more.
When the Turtles drove the Turtle Van into the Ace Chemicals compound, Donatello was put in charge of defending them from a crane controlled by a League of Assassins ninja. He was placed on a raised platform from inside the van, which fired manhole covers at high velocity. He was then attacked by mutated League and Foot Clan ninjas, and was assisted by Robin.
After defeating many enemy ninja, Donatello and Leonardo faced off against Ra's al Ghul in a fight. However, Ra's al Ghul was able to badly break Donatello's arm and throw him off a catwalk. He landed near the device that was about to be launched, and clung to it as it took off. Due to his broken arm, he was unable to do more than hold on to the machine, and was reduced to calling out advice to Michelangelo. When Michelangelo managed to overload the device, he and Donatello fell out of the sky, but both landed safely on a passing blimp.
Upon returning to the Batcave, Donatello's arm was placed in a cast by Alfred Pennyworth, and he began following Batgirl on social media. He then eagerly accepted the offer of pizza from Batman.