During a battle with Shredder, Raphael, 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, Raphael and his brothers attempted to stop them.
These attempts brought them to the attention of Batman, who soon found and fought the Turtles. During the battle, Raphael lost one of his sai to Batman, and was tased by the Batmobile, rendering him unconscious. Afterwards, when Donatello was researching Batman, Raphael expressed distaste for the superhero and extreme concern about potentially being trapped in Gotham permanently.
Raphael 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. Upon reaching the Bat-Cave, Raphael continued expressing his displeasure about Batman and his belief that the superhero was "crazy." 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. When Raphael attacked him, Shredder slashed his shoulder badly, which required immediate medical attention.
After his arm was placed in a sling, Raphael remained angry as his brothers interacted with Batman and Alfred Pennyworth, and eventually erupted at his family for putting their trust in Batman, whom he saw as a rich dilettante who had failed them. He left the Bat-Cave, expressing his intention of getting home without Batman's help.
Batman followed him and eventually convinced Raphael to go to Crime Alley with him, where he told Raphael about the murder of his parents and how it motivated him to fight crime. Raphael was deeply moved by this story, which changed his viewpoint on the superhero.
He then accompanied Leonardo and Batman to a meeting with Commissioner Gordon and the Penguin, who informed them of Shredder and Ra's al Ghul's takeover of Arkham Asylum. Leonardo then collapsed, which shocked and alarmed Raphael.
When a way was found for the Turtles to return home, Raphael stated that it had been an honor to work with Batman. When the superhero was attacked by mutated Arkham inmates, Raphael spoke out in favor of helping him, having gained an understanding of Batman and his attempts to help the Turtles. He chose to remain in Earth Prime and came to Batman's rescue.
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. Before returning to his own dimension, Raphael gave Batman his mask and the assurance that he would be welcome with them if he ever traveled to the Turtles' world.
After the imprisonment of the Shredder, Raphael and his brothers tried to deal with the internal strife of the fracturing Foot Clan. Raphael and Leonardo fought the Elite Guard on a subway car, but were forced to turn back to rescue Donatello from the Elite Guard's leader. Raphael was enraged by the attempt to kill his brother, particularly the man's affirmation that he was doing the brothers a favor.
After Bane appeared in New York, Raphael joined Michelangelo 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, Raphael was initially angry at his brother for inadvertently causing the problems the city was facing. He also developed an immediate antipathy for Robin, who repeatedly expressed disdain for the Turtles and their home, and fought fiercely with the boy.
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. Raphael fought his way to Bane, who was impressed by his fighting prowess and fierce temperament. However, Bane was too strong, and nearly broke Raphael's spine before Splinter could intervene to save his son. Raphael escaped without serious injury, but Splinter was left comatose.
Upon their return to the lair, Raphael agreed with Donatello that they should use Venom to defeat Bane, but they were overruled. He remained at Splinter's bedside until a portal to Earth Prime could be opened, and brought his father through to the Lazarus Pit. He then fought the Ninja Man-Bats alongside his father, Nightwing and Batgirl. Upon returning to his own world, 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. Raphael 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, Raphael posed for a group photo with his friends and family.