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The episode starts in Fogburyport, birthplace of Green Clam Chowder. The Simpson family arrive there because a book stated it's a place to visit before they mysteriously disappear. At an Oyster-Eating Contest they discovers that it's a ruse to get sacrifices for Cthulhu. As Cthulhu is about to eat Homer, he challenged Cthulhu to an eating contest and wins. Chthulhu pukes and asks what Homer wants.
Homer whispers "I want to eat you." Then we see Chthulhu in a giant cooking pot and The Simpsons (except Lisa) enjoying a hot-dog made of Chthulhu's Tentacles. When Homer pokes his ink sac, it explodes, leaving the Treehouse of Horror XXIX logo on the screen.
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The segment begins with an underwater base of Mapple where Steve Mobbs (on a screen) tells about the new Myphone and the new unfunny version of him to a hyper audience. When everyone is on their phone the unfunny Steve is revealed to be a plant alien on a mission. Now on the plant planet they shoot spores to Earth (going right next to the Futurama ship with a cloth saying "BRING BACK FUTURAMA" and then getting blown up by the USS Orville).
In Springfield, everyone is switched with plant copies of themselves. Comic book guy says this is a homage to the movie Body Snatchers while the movie itself was a rip off of The Thing. When a plant version of Comic book guy says "pad" Milhouse and Bart get scared and run away. Bart and Lisa try to run away with Lou in his police car, but are turned. Lisa is brought to the alien world, which is in reality an utopian world where no one uses phones, tablets. She is welcome by Xylem and Phloem, and finds herself in what human calls Crab Nebula. Everyone that was switched from Springfield is also there.
Moments later, the Plant people see the citizens with pods (Mapple products) and ask where they found those. Bart says they found it under the living Christmas tree and thus utopia ruined.
After a sleepover at Milhouse's, Bart, Nelson and Milhouse find themselves in a cell. They are suddenly freed by Lisa, who has developed multiple personality disorder. Turns out, Penelope, one of her personalities, is the one that trapped them in that cell. Penelope acts weird and locks them back in after they don't ask for an encore of her signing performance. Lisa attacks then kills Milhouse and Nelson. As she tries to kill Bart, he asks her what happened to her, to which Lisa tells the story: Bart grabbed Lisa's spelling test, changing her answers, mocking Miss Hoover and granting her a F.
Lisa s normal personality momentarily surfaces and gives Bart one last chance to save himself. He appeals to her better nature and her love as a sister, which frees Lisa and saves him from being killed by her. Turns out Lisa didn t kill Milhouse, just encase him in a block of paper. Milhouse tells her he doesn t mind, since he always wanted to be a "paper boy".
Mr. Burns opens up a Jurassic-themed retirement home, a park filled with elders rejuvenated mixing their DNA with dinosaurs'. He brings Springfielders to the park, showing them the new "retirement home". At first they're all human, healthy and feeling young again, with incredible strength too, but once Homer raises the temperature after Grandpa complains about the temperature being too cold, they transform into dinosaur creatures.
Visitors and Mr. Burns are killed by the elders, while the Simpson family is threatened by Grandpa and Jacqueline Bouvier, but Lisa courageously confronts Grandpa, and find out they all just needed to be cherished and respected. In the end the Simpson family escapes alive and unharmed, though their helicopter is being flown by pterodactyl Agnes.