In Tallahassee, Florida, on December 21, 1999, a memorial service is held for a former FBI agent named Raymond Crouch. His widow is approached by a mysterious man, Mark Johnson, who claims to have worked with her husband. After the other mourners have left, Johnson returns to the funeral parlor, dons the corpse's clothes, and places a cell phone in the coffin. One week later, Johnson is monitoring Crouch's grave when his phone rings; he walks towards the grave with a shovel. Fox Mulder and Dana Scully are called in to examine Crouch's empty grave. They notice damage done to the interior of the casket; Scully theorizes that the scene was staged. A briefing is held by Walter Skinner, who notes that Crouch is one of four former FBI agents whose graves have been exhumed; all four men had committed suicide. Because of the presence of goat's blood encircling the grave, Mulder states that the crime was an act of necromancy. After the briefing, Skinner takes the agents aside and asks them to investigate Crouch's possible ties to the Millennium Group.
Mulder and Scully go to a mental institution in Woodbridge, Virginia, to visit Frank Black. Black is initially reluctant to help the agents, as he believes that any further involvement with the Millennium Group may hinder his custody battle for his daughter, Jordan. When Black agrees to help, he explains that the members of the Millennium Group believe they can bring about the end of the world by killing themselves before the dawn of the millennium. Acting on information from Black, Mulder concentrates on trying to find Johnson, when Scully is attacked in the morgue by the dead deputy. The two agents put all their effort in to finding Johnson before it is too late. The agents search for Mr. Johnson, uncovering information about a bizarre string of reanimated corpses rising from the dead and searching for victims. Mulder later goes to Mr. Johnson's house and is trapped by Johnson in his basement with a group of corpses who rise up and attack him. Mulder is saved when Frank shows up, shooting a number of zombies in the head. As the gun runs out of bullets and death seems imminent for Mulder and Frank, Scully arrives, saving both their lives.
The epilogue shows Frank in the hospital with Scully and Mulder. Scully informs Frank that he has a visitor and brings in his daughter Jordan. Meanwhile, Dick Clark's New Year's Rockin' Eve is on a television in the background as the countdown begins. Frank leaves, and Mulder and Scully are left alone. As the clock strikes zero, and the crowd begins to sing 'Auld Lang Syne' on screen, Mulder and Scully kiss to ring in the new year. (TXF: "Millennium")