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After the death of his wife, Frank moves to Falls Church, Virginia with his daughter Jordan and rejoins the FBI, with the intent of bringing down the Millennium Group. He partners with Special Agent Emma Hollis, a young FBI agent with promise. Other new characters are introduced, including Special Agent Barry Baldwin and Assistant Director Andy McClaren. Throughout the season, Frank discovers more about the Millennium Group's agenda, but since he's now on the outside looking in, his discoveries come less often. Even though Frank has made it clear that he wants nothing to do with the group, Peter Watts still tries to get him back. Emma Hollis' father has an unusual case of alzheimers, which the Millennium Group can cure, if Hollis joins them. And in the end, she does.
|No.||Episode Name / Summary|
Several months after the death of his wife and a nervous breakdown, Frank rejoins the FBI and works with two young agents to investigate a plane crash that seems connected to the virus that killed his wife.
As Frank and his new FBI partner, Emma Hollis, continue to investigate the brutal murders of several similar women, they discover that the deaths are related to the Millennium Group and a secret government project involving remote viewing.
While investigating a fatal shooting at a Seattle high school, Frank Black, Emma Hollis and Special Agent Barry Baldwin learn of a survivalist group that fear the predicted Y2K computer meltdown as they believe it will precede a devastating apocalypse.
Twenty years after she witnessed the unexplained murder of her sister, Emma Hollis works on a case she requested involving a series of disturbingly random killings.
|"...Thirteen Years Later"
A psychotic madman maniac tells how, before and on Halloween, Frank Black investigated a series of confounding murders on the ominous set of a movie based on one of his former cases.
|"Skull and Bones"
After the skeletal remains of a single body are found, Emma works on uncovering more remains while Frank determines that the bodies were victims of the Millennium Group.
|"Through a Glass Darkly"
Frank and Emma struggle to find a missing young girl seemingly kidnapped by a pedophile who was recently released from jail but discover that the truth is darker than they initially suspect.
Suspected of drug abuse and forced out of the FBI, Emma Hollis investigates without legal authority when her drug-addicted half-sister claims that tainted heroin is being sold on the streets of Vancouver and is turning local addicts into monsters.
As Christmas approaches, Frank goes on vacation with his daughter, Jordan, and locates a former killer for the mob who is desperate to protect two young females who have regenerative healing abilities.
With help from Emma Hollis, Frank investigates a deliverer of death who has killed three people by causing them to drown on dry land and is negatively effecting Jordan by making her fall life-threateningly ill.
Members of the FBI, including Frank and Emma, investigate the kidnapping of Peter Watts' daughter, Taylor, who was abducted by an enraged Gulf War veteran attempting to force the Millennium Group into admitting their crimes.
|"The Sound of Snow"
While Frank investigates several suicides, he receives apparently misleading visions of the victims' deaths and sees his deceased wife, Catherine.
Frank once again encounters his demonic nemesis, Lucy Butler, who is deviously working as a nanny for a powerful Wisconsin politician and his wife.
Frank and Emma investigate the suicide of a former FBI agent whose last, unfinished case involved the unexplained murder of a scientist in 1945.
|"Forcing the End"
Frank and Emma try to recover a baby that has been kidnapped by a group organized by people who believe they must prepare for the return of the Messiah at the Millennium.
|"Saturn Dreaming of Mercury"
When a family moves into Frank's neighborhood, Jordan starts acting oddly and makes a new friend called Simon who might not be as imaginary as Frank initially suspects.
While Frank and Emma attempt to locate a young woman who has escaped from a mental institution, Emma discovers that the case may somehow be related to her ailing father, who seems to be losing his mind.
A computer virus leads Frank to a Buddhist temple, where a man terrified of the Millennium Group lies dying due to a disfiguring disease as an agent of the Group hunts for him. Emma discovers that the dying man, a former Millennium Group member, was conducting mysterious biological research and desperately attempts to stop the Group from continuing their experiments.
|"Seven and One"
Frank receives a series of Polaroid photographs showing his face as he drowns, and is forced to confront painful childhood memories while high-ranking members of the FBI become concerned for his sanity.
Emma and Frank travel to a small town in Pennsylvania where a town sheriff, a childhood friend of Emma's, asks for their help in investigating the murders of several young women.
While Emma is approached by Peter Watts with an offer to cure her father if she agrees to help force Frank out of the FBI, Frank pursues a copy cat killer who murders couples while they make love.
|"Goodbye to All That"
Emma agrees to let the Millennium Group help her father, as Frank quits the FBI and leaves town with his daughter.
- Brittany Tiplady as Jordan Black
- Terry O'Quinn as Peter Watts
- Peter Outerbridge as Barry Baldwin
- Stephen E. Miller as Andy McClaren
- Sarah-Jane Redmond as Lucy Butler
- Bob Wilde as Mabius
- Maxine Miller as Justine Miller
- Ken Pogue as Tom Miller
- Trevor White as Doug Scaife
- Jessica Schreier as Barbara Watts