1. The Innocents (1)
The Marburg virus has apparently run its course. Several months after the death of his wife and a nervous breakdown, Frank rejoins the FBI and investigates a plane crash with a new partner.
Millennium — Season 3
2. Exegesis (2)
Frank and Emma investigate a family of identical women who are apparently being killed off.
3. TEOTWAWKI
Frank and Emma investigate a survivalist group worried about the Y2K bug.
4. Closure
Emma is haunted by memories of the death of her sister while she and Frank hunt a spree killer.
5. ...Thirteen Years Later
Frank and Emma investigate murders on the set of a movie based on one of Frank's former cases.
6. Skull and Bones
Frank and Emma investigate a mass grave that may have links to the Millennium Group.
7. Through a Glass, Darkly
The disappearance of a child leads a town to accuse a recently released sex offender who may or may not be guilty. Frank and Emma arrive to determine the truth.
8. Human Essence
Emma tries to help her drug addicted sister and learns that local addicts are exhibiting strange mutations linked to tainted heroin.
9. Omerta
On Christmas, Frank and Jordan go one vacation in Vermont. Unexpectedly, they get involved with a supposedly dead Mafia hit man who appears to be living in the woods with a number of mysterious women.
10. Borrowed Time
Frank and Emma investigate a number of apparent drownings that occurred on dry land.
11. Collateral Damage
Peter's daughter is kidnapped by a Gulf War veteran who hopes to force the Millennium Group into admitting their crimes. Frank and Emma attempt to help, but Peter seems determined not to betray the secrets of the Group.
12. The Sound of Snow
Frank receives a mysterious cassette tape filled with white noise and a visit from beyond the grave.
13. Antipas
Lucy Butler returns to torment Frank. This times she is a nanny for a powerful Wisconsin politician.
14. Matryoshka
Frank and Emma investigate the suicide of a former FBI agent and discover links between the FBI, the Millennium Group, and the Los Alamos nuclear research center.
15. Forcing the End
A fundamentalist Jewish sect abducts a pregnant woman hoping to raise a pure child for the priesthood and force the coming of the Messiah.
16. Saturn Dreaming of Mercury
When a new family moves into town, Jordan is filled with the uneasy knowledge that the devil is near.
17. Darwin's Eye
Frank and Emma attempt to locate a girl who escapes from a mental institution while Emma's father grows ill.
18. Bardo Thodol
Emma and Frank investigate the mysterious biological research conducted by a former Millennium Group member who is dying from a mysterious disease.
19. Seven and One
Frank receives a series of Polaroid photographs showing the face of a drowning victim. The face is his own.
20. Nostalgia
Frank and Emma investigate a murder in a small town where Emma spent part of her youth.
21. Via Dolorosa (1)
Frank investigates a series of murders that replicate a serial killer case from his past while Emma moves closer to the Millennium Group.
22. Goodbye to All That (2)
Frank is held responsible for a man's death while Emma joins with the Millennium Group.