This episode starts out with GIR walking home drinking, or trying to drink, a slurpee. (I really have no clue what he is doing, but that is only my guess.) The scene shifts from GIR to Zim down is his lab. Zim is fixing his backpack when an alarm went off for a security breach. Zim goes upstairs and sees the front door left open by GIR, and Zim starts yelling at him. GIR ignores him and tells him that he got chocolate bubblegum, and while Zim was lecturing him, he looked up and saw someone crawling around on the ceiling, almost cloaked. Zim's finally done lecturing Zim, and Zim is about to go back down to his lab when someone takes a picture of what is happening. It's Dib, and he suddenly falls from the ceiling. Zim chases him around the house and Dib jumps out the window, away from all the danger. Dib starts telling Zim how his alien guts are going to be all around an autopsy table, and the lawn gnomes start to come after him, but Dib is too quick and he makes his mistake.
The next day at skool, Dib and Gaz are sitting at lunch, and Dib is telling Gaz about how Zim didn't show up at school today, and that his secret will be out, and he might go on Mysterious Mysteries and host his own episode. Gaz tells him to shut up and let her finish with her game.
That night at Dib's house, Dib puts his pictures in an envelope addressed to Mysterious Mysteries, and goes into the living room to watch the show. The show comes on and says, "For years, the question about whether aliens exist has been around, and we here at Mysterious Mysteries know the answer to that question, and the answer is maybe." (That was pretty funny, I had to put that in here.) It goes on and tells them to send their proof that aliens exsist, and Zim arms start to move around on their own. They start to hit Gaz, and Gaz gets mad and walks off, playing her game. Dib rips up the envelope and the pictures drop out. Zim comes on the screen, and tells Dib that he is in a microscopic vessel somewhere in his disgusting body, near his arm control nerve. Dib tells Zim that humans don't have arm control nerves, and Zim yells at him not to aggrivate him, that he's controlling his arms, and starts flinging Dibs arms around everywhere. Dib asks Zim how he got inside of him, and Zim says it starts at the cafeteria.
It shows Dib from whenever he was talking to Gaz about the pictures, and how Zim was hiding in the peas, and whenever he ate the peas, Zim was in his spoonful and ate him.
It goes back to Dib's living room, and Zim makes Dib crush the pictures in his hand. Dib tells Zim that he's an idiot, because that was not the original copy. Zim comes back that he's inside his body, and that he can go to his brain and delete the knowledge of where he hid the orginal, and, as an added bonus, make his whole brain not smart. Dib runs downstairs and asks his dad if he still had that microscopic nano-fighter ship he was working on, and Professor Membrane pulls a plastic baggy out of his shirt. He asked Dib why he needs it, and Dib said that there was an alien in his guts and that he's trying to destroy his brain. Professor Membrane tells him to run along then.
Dib runs upstairs and swallows the fightership, and uses the controls like a game to steer around. He sudenlly finds an Irken flag. Dib's ship finally catches up to Zims, and he starts to follow him. Meanwhile Gaz walks in and thinks that Dib is playing an online game. Dib fires something at Zim, but Zim easily maneuvers around that. He tells Dib that he has been flying since before he was born (Sad Little Earth Monkey!) and hits a part of Dib's... Dib. Dib screams that that was his spleeen, and Gaz asked if she could play. Zim gets up to his mouth, but Dib sucked in, and made them fall down more. Zim told Dib to prepare for some doom, and Zim transformed. Gaz told Dib that a transform was alway quarter-circle back. They fought for a while, and Zim hit Dibs arm and leg nerves, so that Dib couldn't play anymore. Gaz, thinking this was just a game, took over the controls.
Zim finally makes it up into Dib's brain, and tries to find where Dib was hiding the disc. He picked a random spot on his brain, and started firing at it. Zim finally told Gaz that he forgot where he hid the file, and Zim said it was time to unleash stupidity on Dib. Gaz finally made it up to Dib's brain, and Gaz started beating the crap out of Zim, all the while, Dib was going crazy, eating a peice out of the couch. Gaz finishes off Zim with a round-house kick in the head, and the robot head went flying off. Gaz beat the game. Dib tells Zim that he had one last finishing move, and he went the the bathroom, flushing Zim down the toilet.