An astronomer, Dr. Lehman (Christopher Lloyd), and his assistant, Imogene O'Neill (Marla Sokoloff), race against time to provide vital information to JPL rocket scientist Dr. Chetwyn (Jason Alexander). Dr. Lehman worked for Chetwyn until Chetwyn fired him, and Lehman is the only one authorized to prevent the impending destruction. Lehman ultimately gets hit by a car and Imogene strives alone, encountering various murderers and automotive failures. Amidst the chaos, Detective Jack Crowe (Billy Campbell) desperately searches for his psychotic ex-partner Stark (Michael Rooker) before the madman seeks revenge against Jack by killing Jack's father and daughter. Meanwhile, Jack's father, the Police sheriff (Stacy Keach) of the town of Taft, deals with subsiding the panic in his town as the meteor shower continues. Another subplot involves a family struggling for survival in a meteor-struck hospital.

After the United States launches numerous nuclear weapons at the approaching asteroid, Imogene discovers a flaw in Dr. Lehman's algorithm and finds that 114 Kassandra had been split in two by the comet that knocked it out of orbit. The second half of Kassandra is larger than the first, and the military's nuclear arsenal is already depleted from destroying the first half, which was believed to be the whole meteor.

As the meteor draws closer to Earth, the meteor storms surrounding it cause increasing amounts of damage as they occur at an unstoppable pace. Part of the headquarters of the scientists tracking Kassandra is hit, resulting in Dr. Chetwyn's death.

Imogene finds herself as the only one left who can save the world from destruction, but she can no longer contact the government by any traditional means of communication. After being abducted by and escaping from Stark with Jack's help, she finds a radio tower that can reach the remaining scientists at the base, but Stark unexpectedly returns, having survived being shot thanks to a bulletproof vest he had previously stolen. By the time Stark is shot dead by the Sheriff and Jack, Kassandra has entered Earth's atmosphere, and the government decides to launch their remaining missiles^{[clarification needed]} and accept the consequences - massive meteor storms and radiation from the blast.

Mere minutes before the missiles hit the meteor, however, Imogene manages to get the scientists to alter their course. Initially it appears that the missiles missed Kassandra entirely, but it quickly becomes clear that Imogene's plan deflected the meteor into the Sun, saving Earth. But three months later, Imogene tells Jack that there will be "next time" in the year 2027, talking about AN 1999, 18 years from 2009.