As Leo Biederman (Wood) and Sarah Hotchner (Sobieski), two teenage astronomy club members, observe the stars, Leo discovers a new object. Leo takes a photo and mails it with the coordinates to astronomer Dr. Marcus Wolf (Charles Martin Smith). Wolf confirms the sighting at an observatory, and after discovering the comet will hit Earth he attempts to alert his colleagues, but is unable to get through. He saves the data to a disk, but dies in a car crash after leaving the observatory.
One year later, Jenny Lerner (Leoni), a field reporter for MSNBC in Washington, DC, is assigned a story regarding the resignation of Secretary of the Treasury Al Rittenhouse (James Cromwell). After Lerner interviews Rittenhouse's wife, who implicates her husband as having an affair with someone named Ellie, Lerner confronts Rittenhouse, who believes Lerner knows about the comet. As Lerner deduces she is on to something more, the FBI apprehends her to find out what she knows. In a meeting with President Tom Beck (Freeman), Lerner agrees not to report about "Ellie" for 48 hours, and over the next two days Lerner discovers that the government was hiding its knowledge about "E.L.E", an acronym for an extinction-level event. In exchange, President Beck gives Lerner the story of a lifetime by allowing her to ask the first questions at a White House news conference...
Beck announces the comet's existence and its track. The comet is seven miles wide, large enough to destroy civilization if it strikes Earth, and that NASA will send a crew of astronauts on the spaceship Messiah to the comet, now named "Wolf-Biederman". Led by Captain Spurgeon Tanner (Duvall), their mission is to destroy it using nuclear weapons.
Ultimately, after a last-ditch effort to use all of Earth's missile-borne nuclear weapons to destroy the comets fails, "Biederman" splashes down in the North Atlantic Ocean near Virginia Beach and Cape Hatteras, creating a megatsunami several thousand feet high. Jenny, her father and Sarah's parents all die, along with others who did not evacuate in time. Coastal cities such as Boston, New York City, Philadelphia, Virginia Beach, Norfolk, Virginia, Charleston, South Carolina, Savannah, Georgia, and Washington, D.C. are destroyed, as well as Atlanta and Florida (as seen from the Messiah spacecraft). Leo, Sarah, Sarah's brother, and many others manage to climb high enough to survive. Later in the movie, we learn that the wave also hit Europe and Africa.
The crew members of Messiah inform NASA of their decision to try to blow up the remaining, larger fragment by flying into a fissure that has formed in the comet and exploding the remaining bombs. They will all die whatever the result, but have enough time to say goodbye to their families. Messiah succeeds in breaking up "Wolf" into small enough pieces that they burn up entering Earth's atmosphere, saving humanity. Afterwards, President Beck gives an inspirational speech, in front of the reconstructed U.S. Capitol building, to begin recovery and rebuilding efforts.