A huge ship appears in the sky of a distant, alien colony and fires a massive beam, transforming the bustling city below to mountains and fields. As the wave encompasses the planet, the ship's crew comment on the colony's erasure before targeting the species' homeworld.
On board Voyager, Captain Janeway is informed by Seven of Nine that the area of space they are currently in belongs to a species that the Borg know as the Zahl. Upon entering this space, though, a small vessel appears off of Voyager's port bow and begins an unprovoked attack. The ship is a Krenim destroyer, and the captain of the vessel (unnamed) barks an ultimatum at Janeway that Voyager must leave "Krenim" space or be destroyed. As the ship's weapons prove useless against Voyager's hull, Janeway ignores the ship and proceeds to negotiate with the Zahl, who disdainfully threaten the weaker Kremin vessel. During their discussion, Tuvok receives ship readings that a temporal disruption involving the homeworld of the Zahl race has just occurred. As they stand there trying to understand what has happened, a wave of temporal energy reaches their sector of space.
The wave hits all three ships - wiping the Zahl race from existence, making the Krenim vessel bigger and more powerful, and reducing Voyager to a severely damaged state. Now cocky and more arrogant, the Kremin captain tells Janeway that Voyager must submit to the Krenim Imperium and prepare to be boarded. Janeway instead takes advantage of Voyager's speed and escapes. A scan of the region in the new Astrometrics bay provides the answer: Krenim warships dominate this region of space and it will be hard for Voyager to sneak past them.
Voyager begins a running battle with many Krenim ships over a period of two months, suffering heavy damages and casualties; even Tuvok is blinded and (non-fatally) burned in one attack. During this attack, Seven of Nine discovers a means of modifying the ship's shields, protecting them from the Kremin chronitron torpedoes. This modification also affects the temporal waves in the region, attracting the attention of the Kremin 'Time Ship', the gigantic ship-based temporal weapon which is causing the temporal waves. Krenim scientist Annorax had built the ship to cause "temporal incursions" to be used to erase events from history in order to strengthen the Krenim Imperium. However, the resulting changes instead caused a plague which killed millions of Krenim, including Annorax's wife, and Annorax has been seeking a full restoration of his species for the past 200 years. Annorax decides to destroy Voyager due to the temporal distortions caused by its shields. The crew manage to escape using the warp drive as Voyager is faster but this causes even more damage to the ship. Janeway is forced to order all but the senior staff to abandon ship as the ship has taken too much damage and can no longer sustain a crew. She and the senior staff remain behind in an attempt to rescue Chakotay and Paris, who were captured by the time ship.