This episode begins right where 200 left off with Cartman, as his hand-puppet persona Mitch Connor, narrating a flashback to Connor's 1972 medical discharge from his Vietnam War tour of duty in a parody of a scene from the film Apocalypse Now as the song "Time of the Season" by The Zombies plays in the background. Back in the present, Mr. Garrison refuses to reveal the identity of Cartman's father, and instead sends Cartman to Dr. Mephisto. Meanwhile, the Ginger Separatist Movement and the townsfolk are negotiating the handover of Muhammad when Mecha-Streisand begins to attack South Park. Muhammad, who is visually obscured throughout the entire episode by a black box superimposed with the word "CENSORED", is taken by Stan, Kyle, and Kenny to Dr. Mephisto's lab. The Gingers arrive and take Muhammad and Cartman captive. The Super Best Friends are called to South Park to help; after their powers fail to subdue Mecha-Streisand, they pacify her by having Krishna adopt the form of Neil Diamond and providing her the opportunity to perform a duet with him.
The Gingers contact the celebrities and offer to share Muhammad in exchange for access to the celebrities' "goo transfer machine", which transfers Muhammad's power to remain free from ridicule to a target individual. Cruise is the first subjected to the process, gaining a "CENSORED" box identical to Muhammad's, but further transfers are interrupted when the Super Best Friends arrive to free their comrade Muhammad. Meanwhile, Cartman is taken to the Ginger lair to meet Scott Tenorman, the Head Ginger. Depicted as a melodramatic madman, Scott has decorated his lair to represent the Chili Con-Carnival in which Cartman gained his revenge on Scott by tricking him into eating his own parents. He reveals to Cartman that they share the same father, former Denver Broncos player Jack Tenorman, meaning that by his act of revenge against Scott, Cartman had killed his own father and fed him to his half-brother.
The fight between the Super Best Friends, celebrities, and Gingers spills over into the Ginger lair, and Tenorman escapes in the confusion. During the fight, Seaman leaps upon Cruise's back, leading Stan to observe, "Tom Cruise has Seaman on his back." The "CENSORED" box over Cruise disappears, and all present continue to make jokes based on the fact that the words "Seaman" and "semen" sound the same. When Cruise questions why they are able to do this leads to a monologue from Kyle, Jesus Christ, and Santa Claus explaining that the goo does not exist, and that threatening people with violence is the only true answer.
As the town begins to rebuild following the Mecha-Streisand attack ("for the 39th time"), Stan, Kyle, and Kenny find Cartman crying – not because he learned that he murdered his father, but because he's "half-ginger". Mitch Connor reminds Cartman that he is "half-Bronco" as well and tells him that makes him "pretty cool" and departs. The boys find Cruise crying for a place in which he can live without fear of mockery. Stan, Kenny and Kyle promise to help Cruise get to such a place. The episode's closing shot is of Cruise's corpse lying on the Moon's surface alongside the corpse of the orca featured in "Free Willzyx".
In the exciting conclusion to this two-part blockbuster celebrating South Park's 200th episode, angry celebrities, violent ginger kids, and Mecha Streisand face off against the Super Best Friends and the South Park faithful. It's a destructive battle on the largest scale but all everyone wants to know is, "Who is Eric Cartman's father?"