NanoZIM: The the Fantastic Voyage.

Dib sneaks into Zim's base one night after GIR leaves the door open, and takes a picture of Zim out of his disguise. He then escapes and plans to send them to the paranormal show Mysterious Mysteries. The next day, Dib is ready to send the disk to the show when all of a sudden he crushes it, and it is revealed that Zim has shrunken himself, infiltrating Dib's body in a micro-submarine hidden deep in his lunch. Dib sends one of his father's microships into his body to combat him, but Zim cheats and attacks Dib directly (attacking his "arm-control nerve...yes, arm-control nerve"), rendering him incapable of fighting back. Dib's sister Gaz then grabs the controls and defeats Zim, but not before she damages Dib's memory, making him forget where he hid the copies of the photograph. Nevertheless, Dib then goes to the toilet and has Zim flushed.

The ending was kinda gross