The Simpson family goes to the Springfield Mall. They all make suggestions on which place to go to, and decide to go with Maggie's idea to go to "Stuff-N-Hug" a store that lets children make their own stuffed animals. Bart finds a stuffed animal that can record your voice, and he gets an idea. When Homer walks by the toys, they start insulting Homer in Bart's voice. Homer gets mad and starts destroying the toys, prompting the family to go home.
Upon arriving, they find their door is open, suggesting a burglar is inside the house. Bart fetches Homer a makeshift weapon made from a cinder block tied to a chain that he calls "The Defender". Homer swings it around to threaten the burglar, but when the family smells apple pie, they discover it is actually Homer's mother, Mona Simpson. Mona says that her days of activism are over, and that she is staying for good. When she asks if Homer will forgive her, a shaken Homer angrily replies that he will not, because of all the times she left him as a child. Homer explains that he feels hurt and abandoned when Mona is not around, and does not want to feel that way again. Later that night, Mona tries to explain to Homer she has changed her ways, but, again Homer does not listen. Afterwards, Homer realizes he should have listened to his mother, and makes her a card as an apology: when he goes downstairs to apologize, he sees her sitting in front of the fire, and asks if she is asleep. When he then notices and questions that she is "sleeping with her eyes open", her head slumps down and Homer realizes that she has died.
Mona is cremated. Homer is distraught, as Mona spent her last hours of life feeling rejected by him. Homer takes Mona's ashes, with assistance from Grampa, who is also so miserable that he says that he originally wanted to dance on Mona's grave after she left, initially he has planned to do the hustle, but had recently been taking tap lessons instead. However he now notes that "I don't feel like dancing" (though as he walks away, taps are heard clicking on his feet). Homer is depressed and guilt-ridden for not apologizing to his mother and struggles to come to terms with her death. Eventually, the family finds and watches a video will from Mona. They discover that Mona left the family some of her possessions: Marge receives Mona's hemp sulfur purse, Bart receives Mona's Swiss Army knife, and Lisa receives Mona's rebellious spirit. For Homer, however, she leaves a task: to take her ashes to the highest point at Springfield Monument Park and scatter them at exactly 3 o'clock. With great difficulty, Homer climbs the mountain in honor of his mother. He releases her ashes, only to find they travel inside the mountain and disrupt a secret nuclear missile launch. Homer is hurt that the last thing Mona told him to do was "one more stupid hippie protest".
Homer is taken captive inside the mountain. There, Mr. Burns explains the purpose of the missile: to send the city's nuclear waste into the Amazon Rainforest. Mr. Burns imprisons Homer in a room, tied up, and returns Mona's ashes (inside of a vacuum bag), to Homer. Outside, the family find Homer and attempt to save him. Bart throws him Mona's knife, which Homer uses to cut himself free. Meanwhile, Marge and Lisa light Marge's hemp purse on fire using a pair of Mona's diamond earrings which Lisa stole. This creates marijuana fumes through a vent, mellowing out the guards. Homer then breaks free from his prison room using "The Defender", and stops the launch. But he accidentally pushes the self-destruct button, exploding the launch site, representing Mona's final victory, through her family, over the things she spent her life fighting.
Homer escapes on a Union Jack parachute landing next to his family. He then releases his mother's ashes once again (after misunderstanding that he only needed to apply water to Mona's ashes to bring her back to life). The scene then turns into clips of Homer enjoying time with his mother from earlier episodes, which ends with a happy Homer as a child hugging his mother over breakfast. The scene then cuts to a black background with white text, saying that the episode was dedicated to Dan Castellaneta's mother, Elsie Castellaneta, and Harry Shearer's mother, Dora K. Warren.