The X-Files have now been officially closed down and Mulder and Scully have been reassigned to different positions. Scully has been assigned as an instructor at the FBI Academy while Mulder is doing menial surveillance work. It is at this time that Mulder is contacted by his friend in the Senate who tells him to go to Puerto Rico to find evidence of alien contact at the large satellite array located there.
Pedro and Sean's relationship has been on the rocks, and Pedro feels that he needs to get away. He heads to Miami to visit his family, where he feels at home. Pedro hangs out with his two best friends to unwind. During his visit home, Pedro gets very ill. He visits a doctor and tries to get lots of rest. His family and roommates are all very worried about Pedro's health. Cory and Puck spend time together to reflect on the house situation. Puck feels that the roommates care more about Pedro than him. Pedro confronts Cory about their misunderstandings.
Storm's unfettered weather-fury continues setting the stage for the rise of Garokk. Even if Storm can be brought back under control, the Sun God's geothermal rejuvenation will spell an end to the Antarctic paradise known as the Savage Land.
Family loyalties are stretched to breaking point when a young tearaway is forced to choose between saving his brother and freedom. And Charlie has a decision to make which will change his future ?- and that of the department.