In the interest of protecting Gotham, Robin spied upon a meeting by Ra's al Ghul and Shredder and returned to the Batcave to inform his father. However, he found the Turtles there instead, and was particularly incensed to see Michelangelo wearing a spare Batman cowl and cape. He fought the Turtles but ended up pinned to the floor until his father returned.
Later he educated Raphael on the League of Assassins, Ra's al Ghul and Shredder's desire for a Lazarus Pit. When the Turtles were served pizza by Alfred, Robin was hopeful of enjoying a slice himself, but was disappointed when his father said they didn't have time for it.
When the group entered Arkham, Robin accompanied Raphael and Michelangelo in the search for hostages. They encountered and fought Mr. Freeze, who had been turned into a polar bear, and eventually eluded him. They also encountered Poison Ivy, but she proved unable to fight them because she had become rooted to the floor.
Robin and Michelangelo tried to take down Mr. Freeze again when the villain attacked Batman, but were thrown into a wall. When Batman was mutated into a crazed bat creature, Robin tried to get through to his father, but Batman did not recognize him. He fought Harley Quinn and eventually defeated her to reclaim the retromutagen that would cure his father.
A recovered Batman was adamant that the Turtles were too undisciplined to accompany him, Batgirl and Robin into combat, but Robin insisted that they were brave warriors and should come with them. He rode to Ace Chemicals with the Turtles in the Turtle Van, and fought mutated ninjas alongside Donatello. He also leaped towards a mutant Tyrannosaurus Rex and demutated him into his human form again.
Robin fought alongside his father, Batgirl and the Turtles at Ace Chemicals, and challenged Baxter Stockman to a fight. To his disappointment, the mutant fly begged for his life, threw up and fainted rather than fighting. When the Ace Chemicals building exploded, he dragged Stockman to safety.
After returning to the Batcave, Robin said goodbye to the Turtles, particularly Raphael. When Batman revealed that he had gotten pizza for the Turtles, he handed Robin a slice, which he eagerly ate.