Voyager christens its new Astrometrics Lab, which has mapping technology far more accurate than their old system. It projects a course that will cut years off their trip, taking them through Zahl territory, which a species called the Krenim also lay claim to. The Zahl tell Voyager not to worry about the Krenim, who once dominated the region with deadly temporal weapons; the Zahl defeated them years ago. Suddenly, Voyager's sensors detect a build-up of temporal energy, and the ship is hit by a space-time shockwave. The Zahl disappear, along with the crew's memory of them, and they find themselves facing the powerful Krenim. Chronoton-based Krenim torpedoes, which exist in a state of temporal flux, penetrate Voyager's shields, badly damaging the ship.

In another part of the region, Annorax, the Krenim captain of the ship that annihilated the Zahl, evaluates his efforts and learns he has almost completely restored the Krenim Imperium. But Annorax will not rest until every colony is back. On Voyager, Janeway manages to destroy the Krenim ship attacking her, but the damage is done. The ship is incapable of continuing its journey. Seven of Nine finds an active warhead lodged in the hull. Tuvok surmises it will explode in minutes, but Seven is intent on learning its temporal variance and using that knowledge to perfect shielding against it. She makes a determination just before the torpedo blows up.

Seven's new temporal shields hold against Krenim torpedoes. In another part of space, Annorax fires his temporal weapon, and the space-time continuum is again altered. This time, Voyager's shields protect it from time disruption. Suddenly, they find that the big Krenim warship they were battling has become a much smaller ship. Annorax's weapon has caused the Krenim Imperium to revert to a pre-warp state. Annorax realizes that Voyager's temporal shields were responsible for throwing off his calculations. He approaches Voyager and transports Chakotay and Paris to his ship for study. He then unleashes a chronoton energy beam to erase Voyager from history, but the starship is able to escape, albeit with major structural damage. Janeway is forced to evacuate the crew, but she and the senior staff stay with the ship to rescue Chakotay and Paris, and hopefully reunite with the escape pods ...