Plot

A former FBI profiler with the ability to look inside the mind of a killer begins working for the mysterious Millennium Group which investigates serial killers, conspiracies, the occult, and those obsessed with the end of the millennium.

After recovering from a serious mental breakdown, former top FBI profiler Frank Black, who has a strange gift that lets him see how a killer's mind works, returns to his hometown of Seattle with his wife Catherine, a clinical social worker who mostly works with victimized children, and their lovable little daughter Jordan, the two people Frank cares about the most in the world, to work as a consultant for the mysterious Millennium Group, a secretive private organization that hires experts to mostly hunt down serial killers obsessed with doomsday prophecies. Frank's partners include Peter Watts, a friend from the Group who serves as his handler, Frank's old friend Lt. Bob 'Bletch' Bletcher from the Seattle Police Department and sympathetic SPD detective Bob Giebelhouse, who also occasionally asks for Frank's help. In season 2, Frank partners up and befriends with the group's latest recruit, Lara Means, a young woman troubled by a gift similar to Frank's. In season 3, Frank partners up with the young dedicated FBI agent Emma Hollis who wants to prove herself to him, which sometimes backfires on her. Most of the cases Frank works on involve killers, lunatics, conspirators and amoral people with criminal intent. However, Frank, who does not believe in the supernatural, must also deal on occasion with those who may or may not be of an actual demonic or angelic nature and not simply evil. Frank's loyalties end up being tested time and time again by both the other-worldly and the Group, which itself seems to be obsessed with the upcoming end of the millennium.

After finally recovering from the complete mental breakdown caused in part by his obsession with a case that almost cost him his sanity, former brilliant FBI profiler Frank Black, who has a strange gift that lets him see how a killer's mind works, returns to his hometown of Seattle with his wife Catherine and their lovable little daughter Jordan, the two people he cares about more than anything else in the world, to work as a consultant for the mysterious Millennium Group, a well-connected conspiratorial private organization that hires experts to investigate predominantly criminal cases involving the occult with special focus on serial killers obsessed with doomsday prophecies. Frank's friend Peter Watts, who suggested Frank to the Group in the first place, serves as a liaison between Frank and the Group and no one, including Peter himself, is really sure where Peter's loyalties truly lie between the two. Frank's old friend Lt. Bob 'Bletch' Bletcher from the Seattle Police Department also asks Frank for help on occasion, and vice versa. Sympathetic SPD detective Bob Giebelhouse and his men also assist Frank in his investigations. Although the cases Frank gets to deal with mostly involve human monsters, lunatics, conspirators and amoral people with criminal intent, Frank, who refuses to believe in the supernatural, also ends up occasionally facing those who may be something more than simply evil. This especially comes into play when he meets his potential archnemesis Lucy Butler, an evil mastermind with strange diabolical goals who loves mind games and may or may not have demonic powers. This issue returns during one especially grim and introspective Halloween night when it becomes clear that something other-worldly wants Frank and is apparently ready to bargain with him over this. Meanwhile, Catherine, who works as a clinical social worker, deals with a few difficult cases of her own usually involving victimized children. Over time, Frank starts to fear that Jordan may have inherited his gift, which he personally always saw as little more than a curse and which he blames for his mental breakdown as he believes that the gift eventually drives those who have it insane if they give into it. On the other hand, Catherine, who loves Frank but cares for Jordan even more, starts fearing that Frank's return to the grim world of crime-solving that sometimes involves psychopathic criminals from his past may eventually cause him to have another breakdown that he won't be able to recover from this time. To make matters worse, a sinister mysterious stalker regularly sends Frank pictures of his family to show him that he's being watched. In time, Frank begins to question his decision to join the Group as more and more evidence surface that they too are some kind of dangerous doomsday cult obsessed with the upcoming end of the millennium, although Peter continually insists that the Group's interests solely lie in preventing potential doomsday scenarios and nothing else.

In season 2, Frank ends up frequently partnering up with the Millennium Group's new recruit, Lara Means, a tough, likable and somewhat troubled chain-smoking young psychic with visions of angels who warn of impending doom. They quickly befriend each other but Frank becomes worried that Lara may be more susceptible to her gift which might cause her to suffer the same fate as him when his sanity collapsed if she continues to work for the Group. Around this time, a friendly hermit known only as "the Old Man", who also happens to be one of the oldest members of the Group, reveals to them more about the history and the role of the Group in the great scheme of things as well as the fact that the group actually has two factions who are now on the brink of war with each other. Things complicate when Peter asks Frank and Lara to pledge their allegiance to the Group and become its full members, which is something that Frank had constantly been refusing to do without knowing more about their true goals. When a mysterious plague breaks out and causes apocalyptic devastation, Frank is put to the ultimate test.

In season 3, the now gray-haired Frank accepts his old job back as an FBI consultant and gets a young partner named Emma Hollis, a dedicated FBI agent who wants to prove herself to everyone, especially Frank and their obstructionist boss Assistant Director Andy McClaren, which happens to be her biggest fault as well. At home, Emma must care for her ailing father who's suffering from dementia and whom she loves very much despite the fact that he can often become very violent towards her due to the disease and is slowly losing the ability to even recognize her. Peter secretly contacts Emma in an attempt to gradually gain her trust and recruit her into the Millennium Group.

Throughout the series, all members and associates of the Group including Frank, Peter and Lara use the Group's special custom-made screensavers that show the countdown to the year 2000. Due to its abrupt cancellation in 1999, the show ends prematurely on a semi-open ending with Frank finally leaving the city after suffering one betrayal too many and burning all his bridges behind him, while Peter ends up paying the ultimate price for his misguided loyalties.

Frank returns one final time in the X-Files episode called Millennium that's set on the very eve of the year 2000, or the new millennium, and symbolically serves as the unofficial Millennium series finale in which Frank must help agents Mulder and Scully stop four zealots from the now disbanded Millennium Group who plan to start the zombie apocalypse.