While visiting family for Christmas at her brother's San Diego home, Scully receives a mysterious phone call that leads to the investigation of a woman's suicide and a young girl who may be the daughter of Scully's deceased sister Melissa.
Scully deeply wants to adopt three-year-old Emily Sim, only to discover that the young girl has developed a serious illness. Mulder arrives in San Diego to help investigate what may be a sinister conspiracy behind it.
Robert Patrick Modell, aka "Pusher," has recovered from his injuries and escaped from a prison hospital. Mulder and Scully lead the manhunt even as Modell may be using his powerful mind-control capabilities to target Fox for revenge.
A teenager becomes the prime suspect in his stepfather's odd murder. Mulder is not buying it since the man was literally swallowed by the ground. After another parent is killed, the suspicion falls on someone close to the kids.
Scully undergoes hypnosis to recall her experiences on the bridge where the group of abductees was burned alive. Krycek provides the consortium with a vaccine for the black oil and tells Mulder of the planned colonization and alien rebels.
In 1990 Mulder investigates the death of a man who disappeared in 1952 before he could be charged in a series of bizarre killings. The retired agent who worked the 1952 case recounts the facts to Mulder and the connection to his father.
Mulder goes undercover to infiltrate a militia group armed with a deadly pathogen and wanted for domestic terrorism. Scully becomes suspicious when Mulder lets a suspect escape but she learns that his assignment may be a suicide mission.
A government assassin is caught trying to kill child chess prodigy Gibson Praise during an international chess tournament. Mulder's old flame Agent Diana Fowley arrives to help on the case but Scully is suspicious of her.