When Shredder made an alliance with an unknown person in Gotham City, Raphael 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. Raphael became frustrated over the failure of their mission, and clashed with Leonardo over their actions. He also kicked several of the Penguin's henchmen off a rooftop, disregarding their safety.
Their efforts brought them to the attention of Batman, whom Raphael recklessly charged at, sparking off a fight between all four Turtles and the hero. Raphael lost his sai and was tased during the course of the fight. After the Turtles escaped, he argued that Batman was Shredder's new partner.
The Turtles made their way into the Batcave, where Raphael and his brothers fought with Robin, until Leonardo was able to explain what was happening to Batman. After that, Robin educated Raphael on the League of Assassins, and Batman gave him his sai back.
Upon hearing of the Arkham Asylum inmates taking over the facility, Raphael 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, 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, Raphael's rash attempt to save a hostage led to himself and Leonardo being electrocuted. This led to Batman being transformed into a crazed mutant bat, which Raphael tried to restrain so he could be dosed with retromutagen. After the superhero had reverted back to his human form, Raphael realized that the entire Arkham incident had been a diversion from Shredder and Ra's al Ghul's true plans.
When a recovered Batman voiced his intention of stopping his enemies without the Turtles, Raphael refused to accept it. He began describing his similarities to Batman, and how he often tried to handle enemies by himself, but how he always needed his brothers to bail him out. His impassioned speech impressed Batman, who agreed to go into battle with the Turtles.
When the Turtles drove the Turtle Van into the Ace Chemicals compound, Raphael and Batgirl rode motorcycles as they fought League and Foot ninja. When Robin demutated a mutant Tyrannosaurus Rex, Raphael caught him.
Raphael then drove his motorcycle through a window at the Ace Chemicals facility, where he fought more ninja enemies. When Shredder had attacked and cornered Batman, Raphael threw himself at Shredder, shattering his mask and saving Batman's life. After Shredder's apparent death and Ra's al Ghul's defeat, the Turtles and Batman left the chemical factory as it exploded.
Back at the Batcave, Raphael exchanged compliments with Robin, admitting that he liked the boy. He then eagerly accepted the offer of pizza from Batman.
- Unlike his past incarnations, Raphael carries his sai sideways on his carapace, rather than pointing downwards and tucked into the front of his belt.