When Malcolm and his brothers destroy their Christmas tree ornaments, Lois punishes them by canceling Christmas and moves all the presents into the garage. The only way she will reinstate the holiday is if the boys behave impeccably up to Christmas morning. Her plan works better than expected, and Lois is touched that her family responded so well to her challenge. Meanwhile, the boys decide that Lois could use this tactic for future holidays and retaliate by breaking into the garage and opening up all the presents. Elsewhere, Francis is forced to visit his Grandma Ida for Christmas.

Bart orders a model rocket and Homer builds and tries to launch it. With help from some nerds and a hamster named Nibbles, a new rocket is built and launched, but results in the church being destroyed. The church looks to rebuild and Montgomery Burns offers his help, but only if he can run the church like a business. The over commercialization of the rebuilt church puts Lisa off; she leaves it for good in search of a new place to worship. She finds Lenny, Carl and Richard Gere at a Buddhist temple. Richard gives her some information about Buddhism and she converts. The family tries to use Christmas as a means to bring Lisa back to Christianity. Realizing what they are doing runs to the temple but learns from Richard that Buddhism allows for the tolerance of other beliefs. So as Homer puts it, she can "pay lip service" to Christianity while remaining a Buddhist.

Buck Strickland has to build a house for Habitat for Humanity as part of his community service, Hank does all the work. Buck is so pleased that he promotes Hank to manager, but when Hank tells Buck in public that he loves him, he is quickly demoted. Cotton becomes jealous that Hank likes Buck better, and Peggy sets out to repair their broken relationship for a Christmas miracle.

Jack has to save Sydney after Sloane ordered for her to be tortured and killed after she is suspected as the SD-6 mole. Meanwhile, Sydney tells Vaughn about her recent time at SD-6, but comes to shock when he gets her a Christmas present. Also, when Will is listening to a tape, he hears SD-6, and decides to do some research, which is not the best idea.

When a stunt on a local cable reality show goes horribly wrong resulting in a man's death, Doggett and Reyes investigate. But when flies pour out of the victims eye sockets, they find themselves relying on Scully's expertise and ask her to join the investigation.

Ashley gets fed up after constantly seeing Jimmy everywhere she goes. She decides to break up with him, but doesn't because it's Jimmy's birthday, and his parents are away- again. Jimmy finds out, and breaks up with Ashley. Meanwhile, Emma has her period at school while wearing a white skirt.