While watching The Itchy & Scratchy Show, Bart and Lisa notice their TV begin to show distortion. Getting some tools (and a chainsaw) to fix it, they return and see Itchy and Scratchy literally leap from the screen and into the living room. The pair trash the room and escape, leave holes in their shape in the wall. Naturally Homer and Marge assume Bart did the damage, and despite Lisa's protests ground him from attending a public appearance of Krusty the Clown.
While Bart stays home, the rest of the family attend the appearance at the Power Plant where nearly all of the city has gathered. As Krusty appears on stage, Itchy and Scratchy show up continuing their ongoing rampage of destruction. The crowd thinks that their just a surprise bonus set up by Mr. Burns While Burns enjoys the crowd cheering him, Smithers warns him that the cat and mouse have reached the reactor core and are causing it to explode. The pair quickly attempt to escape in a helicopter before the blast.
Meanwhile, Bart has chosen to take advantage of the lack of people to have some fun in his guise of El Barto and is graffiti tagging everything in sight. As the power plant explodes in the distance, he see the explosion, and changes into Bartman to investigate. There he sees that most of the population have become super-power beings as a result of the explosion after facing various Springfieldians, including his family, and after a brief battle gets the instinctive urge to head for home.
As Bartman arrives near home he sees a spaceship in the Flanders' backyard. As he investigates he runs across Kang and Kodos who as fans of Itchy and Scratchy themselves, caused their appearance in Springfield thanks to one of their devices. Locking Bartman in a cage so he can be a pet, they leave to watch the cat and mouse's antics at Barney's Bowlarama After trying to send a signal to Milhouse with no success, he gains a brief flash of genius and uses his cage's giant hamster wheel to escape.
Back at home he uses the alien device that he stole to try to bring Radioactive Man to life as well to help him. After his first attempt with the TV version fails, he succeeds with Homer's old video camera and one of his Radioactive Man comics. With the superhero's help he again faces the various supers in the city, with little success. After another flash of genius, he heads for home with Ned Flanders' video camera in hand.
Bartman and Radioactive Man attempt to alter the alien device so that with the film footage on the camera they can travel back to the point before this all started and stop it. However, it turns out that the aliens arrive looking for the device and parts the pair stole from the ship. They reveal that the final component was in their immediate possession all along and that Radioactive Man stole the wrong one. After blasting him they turn on Bartman, who's only saved by a last minute appearance by Milhouse, who's come to his senses just in time. Just before pulling the switch Bart reveals that his brilliance was in reality that of his sister Maggie who was given super-intelligence by the blast and sent her brother messages telepathically.
Bartman pulls the switch just before Itchy drops a large bomb, with Scratchy attached, on the city. Bart suddenly finds himself where he was moments before the cat and mouse escaped from their TV. When the TV distorts, Bart turns it off before the pair appear claiming he had seen the episode before. As a result, this causes Kang and Kodos' machine to backfire, and they leave the planet angrily, which erases all previous events of the comic [and presumably Bart's punishment]. Only Bart has full memories of the incident with the only sign it happened being that the ending of the comic he pulled Radioactive Man out of has changed due to giving Bart his membership card to the Superior Squadron as a souvenir.