Snake is arrested for smoking inside the Kwik-E-Mart. Chief Wiggum explains that as this is Snake's third strike, he will be executed in accordance with the new law. Before hauling Snake away, Chief Wiggum helpfully points out that Apu, Moe, and Bart are all witnesses; Snake vows to kill all of them. Snake is executed in the electric chair on World's Deadliest Executions, hosted by Ed McMahon and proudly broadcast on Fox, while Homer, who's watching on TV, complains that they only do crucifixitions during sweeps. Chief Wiggum sends the body to the hospital to be used up for organ donations (Barney calls out "dibs on the liver").
Shortly afterward, Homer visits Dr. Nick, who transplants Snake's hair onto Homer's head. When Homer goes to sleep the following night, it plants its roots in Homer's brain. With the hair controlling his mind, Homer (who begins to speak with Snake's voice) murders Apu by drowning him in his own Squishee machine. The next day, Homer goes to Moe's Tavern, where he removes Moe's heart with a corkscrew. Bart realizes that the other two witnesses have been killed, and Homer vows to protect him. Homer locks himself and Bart in a room, but Snake's hair takes control of him. Homer tries to kill Bart with a sledgehammer. Bart begs Homer to fight the hair and, after a struggle, Homer rips the hair off his head. The hair tries to smother Bart (like the Facehugger) and Homer tries defending Bart by punching the hair, though due to it being attached to his face, all this does is hurt Bart.
Wiggum bursts through the door with the intention of arresting Homer for the murder of Moe (not being able to say Apu's last name, he settled for just the murder of Moe). Homer states the hair is the killer, which makes a jump for the window. Wiggum opens fire and the hair is shot dead. Maggie picks up the hair and cuddles it close like a stuffed animal. Chief Wiggum jokes "now that's a bad hair day"; everyone laughs except Marge who reminds everyone that two well known people of Springfield have been murdered, only to suddenly get the joke, and joins in with the laughter.
Marge forbids Bart and Lisa from watching the Itchy & Scratchy Halloween special, and takes the batteries out of the TV's remote control. When Marge leaves, Bart finds a small piece of highly unstable plutonium in Homer's toolbox and hammers it into the remote's battery slot. When they use the remote, the kids actually enter the world of Itchy and Scratchy after they accidentally press the Enter button while Lisa tries to get the remote control from Bart. They watch Itchy decapitate Scratchy and use his head as a jack-o'-lantern. While the two laugh, Scratchy's head asks why Bart and Lisa are laughing to which Itchy replies that they are laughing at his pain. Because of this, Scratchy reattaches his head and forms a partnership with Itchy to "teach them a lesson". Back in the Simpson house, Homer enters the living room and watches the show. Bart and Lisa go through life-death situations such as Itchy lighting up a cannon while Scratchy loads it with various weapons. Homer (oblivious to what he sees on the TV) decides to change the channel, and Bart, Lisa, Itchy and Scratchy wind up on Live with Regis and Kathie Lee.
Afterward, they end up back at Itchy's house and urge Homer from inside the TV to use the remote to get them out. While Homer is figuring out which button to press, Itchy and Scratchy unleash a hose full of piranhas at Bart, which eat away at his body until it is a skeleton (although his head remains uneaten). Homer finally picks the right button and zaps them both out and Lisa then presses the rewind button to return Bart's body to normal. Unfortunately, Itchy and Scratchy also escape from the TV into the real world, armed with axes. At first, the family is scared, but realize how small the two characters are (the size of a regular mouse and cat respectively) and decide to keep them as pets. Itchy ends up in a hamster cage and Scratchy has fallen in love with Snowball II. However, much to his terror, Marge says he has to be neutered.
When Maggie refuses to eat her oatmeal, the Simpsons discover she has gotten her first baby tooth, which appears to be a sharp fang. Later, when Homer is playing 'This Little Piggy' with Maggie, her legs fall (which Homer believes she lost her 'baby legs') before growing green tentacles and climbing onto the ceiling while hissing, swinging Homer around the room when he tries to get her down with a broom. Dr. Hibbert, who can't explain what's happening to Maggie, prescribes lots of fire to Homer and Marge (which Marge says is his cure for everything).
As Lisa comments that she wish Maggie could tell them what was happening to her, Maggie begins sucking on her pacifier in a rhythmic way, which is actually a message to the alien duo, Kang and Kodos to inform them her larval stage is complete. They arrive at the Simpson house, coming to retrieve Maggie. Marge reveals that Kang is Maggie's real father, much to Homer's shock and anger (and worry that Kang was a better lover). Marge retells the story: Kang and Kodos abducted her while she was doing laundry, selecting Marge for a cross-breeding program. She says the aliens used mind-control techniques on her. In reality, the entire process consisted of Marge and Kang sitting on a couch, Kang quoting terrible pick-up lines only to suddenly pull a "look-over-there" and use a ray which impregnates Marge as she looks. She recalls that nine months after the abduction, Maggie was born.
Kang and Kodos demand that the Simpsons give Maggie to them, and Kang and Homer start to fight over Maggie until Bart stops them and tells them there is only one place where something this bizarre can be resolved: The Jerry Springer Show, where the episode is entitled "My Daddy is a Space Monster". On the set, Homer and Kang continually fight, throw chairs, and curse (which is naturally bleeped out). When an audience member criticizes Kang for not being around for Maggie after he impregnated Marge, Kang vaporizes her, much to Jerry's chagrin, and when he says that Kang can't do that to his audience, Kang takes it as a challenge and vaporizes the rest of the audience and the film crew. During Jerry's "final thought", Maggie attacks Jerry Springer, to which he swears at the baby, resulting in an angry Kang beating him to death while Homer continues to punch Kang.
After leaving the studio, Kang and Kodos threaten to destroy every politician in Washington unless given Maggie. Marge and the Simpsons slyly imply that the aliens could not possibly destroy every politician, and they fly off to do so.