When Dr. Albright announces she is going to Borneo for a year, Dick decides to ask her to marry him. Because of his anxiety Dick experiences his first nightmare leading the other aliens to believe that Dick's brain is breaking down creating more anxiety and nightmares for Sally and Tommy. Harry contacts the Big Giant Head so they can return for emergency maintenance. Dick decides to stay behind and risk dying as a human than to go back and chance not returning in Mary's lifetime.

Bart's class goes to the police station on a field trip and while he is there, he just can't resist pulling a prank; meanwhile, Lisa's class is not challenging for her at all. Chief Wiggum meets with the Homer and Marge and recommends military school for Bart. Homer and Marge tell Bart they are going to Disneyland, but trick him and take him to military school. Bart does not want to be there from the get-go, but Lisa sees the discipline the cadets receive and decides to stay there with Bart. She is the first female ever to join the academy, so she gets a hard time from the other cadets. Bart starts to fit in after a while, and tries to keep the fact that he cares about her a secret. A final challenge awaits Bart and Lisa; they must pass a physical test called "The Eliminator". Bart helps Lisa to train in secret and when they both pass, they go home.

When Dr. Albright announces she is going to Borneo for a year, Dick decides to ask her to marry him. Because of his anxiety Dick experiences his first nightmare leading the other aliens to believe that Dick's brain is breaking down creating more anxiety and nightmares for Sally and Tommy. Harry contacts the Big Giant Head so they can return for emergency maintenance. Dick decides to stay behind and risk dying as a human than to go back and chance not returning in Mary's lifetime.

While investigating the discovery of a preserved alien body found in the mountains of Canada, Mulder is contacted by Michael Kritschgau. He tells Mulder about a government conspiracy to make people believe in aliens without question, and Mulder has been the prime target.

Murphy makes a candid comment about the President during the end credits for FYI that goes out on the air. When Murphy refuses to apologize, Lansing fires Kay. The next day, Murphy receives a phone call and is summoned to appear at the White House, where she sits and waits. Murphy returns from her audience with the President; she has a big decision to make regarding her future.