In 1979, a newborn girl named Christine York is identified by Satanist—including her doctor, Dr. Abel, and her guardian, Mabel—as the one chosen to bear Satan's son during the last hour on New York Eve, 1999, due to a symbol on her arm. As she is being born, a priest in thevatican witnesses a comet, described as the "Eye of God", heralding the birth of the one chosen to be the mother of Satan's child. The priest is then sent on a mission by the Pope to find and protect the girl from Satan's presence at all costs. However, a few Vatican Knights (led by a corrupted cardinal) insist that she must be killed to prevent Satan's plans, which most of the clergy (including the Pope) opposes, as they view that taking a life in an attempt to stop evil is sinful.
Twenty years later, near the end of 1999, retired cop Jericho Cane, in a constant state of depression since his wife and daughter were murdered by hit-men, is assigned to protect a Wall street banker; Jericho now works for an elite security and protection company. They are attacked by a priest named Thomas Aquinas, who is eventually captured and taken to a hospital. Unknown to Jericho, Aquinas somehow knew the real identity of the banker—he has been possesed by Satan and now wields great powers. Satan locates Aquinas and brutally murders him, crucifying him onto a ceiling. Jericho and his co-worker/friend Bobby Chicago see a name amongst many other things scratched into Aquinas's skin, and after some guesswork, begin searching for Christine York.
Jericho and Chicago find the now-adult York in her apartment and save her from the Vatican Knights who attempt to assassinate her. That evening, Chicago waits in a van while Jericho discusses the recent happenings with Christine. Satan arrives and blows up the van, killing Chicago. As Jericho and Christine try to flee, they are apprehended by Mabel who is possessed with preternatural strength despite her late middle age and lesser size. Jericho barely manages to subdue her. Outside, Marge, Jericho's superior from his days in the police force, and another police officer—both Satanists—confront him, demanding Christine. Jericho kills them both. A few moments later Satan resurrects Marge for her usefulness as a NYPD detective to have the police search for Jericho and Christine, who have escaped to a nearby church, seeking answers from a priest, Father Kovak.
Kovak soon realizes Christine and the banker's roles, and describes how at the end of every millenium, Satan will possess a man's body to consummate with the flesh of a preordained woman. If he succeeds in taking York, he will have free rein over the world. After hearing that the only way to defeat Satan is to "have faith", Jericho tries to persuade Christine to go into hiding with him, but she prefers to stay with Kovak after he says that Satan's greatest trick was to fool Mankind that he did not exist and she felt Kovak's explanation was true. Frustrated, Jericho returns to his apartment, and it is there that Satan meets with him and tries to tempt him with his lost family and his anger at God in order to make him reveal Christine's location. Jericho resists and manages to throw Satan out of his apartment window. Chicago soon shows up, alive and well. Despite Jericho's initial suspicion, they make a plan to retrieve Christine.
At the church, where Kovak and his clergy informs the Pope of York's location, he orders them to hide and protect her at all costs. Unfortunately, the Vatican Knights arrive again, taking Kovak and his clergy into custody while they try to kill Christine again. Before they manage to do so, however, Jericho comes by and stops them, saving Christine and the clergy. Satan then appears, and Jericho runs away safely with Christine. The clergymen, in an act of bravery, confront Satan and try to send him back to Hell by using exorscism, but he resists them with impunity, killing the Vatican Knights, including the misguided cardinal. As Jericho and Christine arrive outside, Chicago then betrays the two; he leaves with Christine while Jericho is beaten by a mob of Satanists and left for dead. The next morning, Jericho is found and rescued by Kovak. Jericho immediately arms himself heavily to resume his search for Christine. He notices the resurrected Marge and follows her to Satan's hidden temple. There, he manages to rescue Christine and kill Marge for the second time. Chicago steps in to stop Jericho, revealing that Satan resurrected him in exchange for his help in capturing Christine. He manages to fight off Satan's influence after some persuasion by his friend; in retaliation, Satan burns him alive. Enraged, Jericho opens fire on Satan and escapes with Christine in the ensuing chaos.
The two make their way through Satan's hideout and into a subway tunnel. They board a train and attempt to escape. Satan catches up with them and kills the motorman. In the ensuing fight, Jericho fires an M203grenade launcher at Satan, wrecking the train and buying them enough time to escape. The banker's body is now irreparably damaged and so Satan leaves it to find a new host.
Jericho and Christine escape to the streets and into another church where he prays to God. Satan smashes through the floor and confronts Jericho in his true form: a massive, demonic creature. He enters Jericho's body and possesses him. Now controlled by Satan, Jericho attempts to rape Christine, but with the help of her begging words, he is able to fight Satan's control for a few seconds. Using what may be his only opportunity to redeem himself, Jericho impales himself on the sword protruding from a fallen statue of Michael the Archangle, thus disabling his body for the few remaining seconds before midnight. At the stroke of midnight beginning the year 2000, the will of God frees Jericho's body from Satan's control and sends Satan back to the depths of Hell forever. After being granted a vision of his wife and daughter smiling and waiting for him on the "other side" (Christine also sees them), Jericho dies contented. Christine thanks the deceased man for saving her life as New York celebrates the start of the new millennium.