According to the Turtles' ending, Krang attempted to send them to Dimension X to prevent them from interfering in his invasion of Earth. However, the Turtles instead ended up on a parallel Earth being menaced by Brainiac. Along with his brothers, Raphael fought a variety of heroes and villains.
After Brainiac was defeated, the Turtles were given a "Super Salty Pizza" by Harley Quinn; this pizza had been treated with the nanotech 5-U-93-R, temporarily turning them into "ultra-turtles." Returning to their own dimension, the Turtles were enhanced enough that Raphael was seen punching a Foot ninja high above his head with little visible effort.