Set in the 24th century, the series follows the adventures of the Starfleet and Maquis crew of the starship USS Voyager after they were stranded in the Delta Quadrant far from the rest of the Federation. In this episode, Voyager is subjected to several changes in their timeline as an alien ship commander attempts to re-sequence history to his liking.
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 (Kate Mulgrew) is informed by Seven of Nine (Jeri Ryan) 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 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 Krenim vessel. During their discussion, Tuvok (Tim Russ) 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 aggressive and more arrogant, the Krenim 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; during one attack, Seven of Nine uses an unexploded Krenim chroniton torpedo to devise a method of successfully shielding Voyager against the weapons, however the weapon partially explodes, blinding and severely burning Tuvok. This modification also affects the temporal waves in the region, attracting the attention of the Krenim "Time Ship", the gigantic ship-based temporal weapon that is causing the temporal disruptions. Krenim scientist Annorax (Kurtwood Smith) 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 also cause a plague that kills millions of Krenim, including his 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. She and the senior staff remain behind in an attempt to rescue Commander Chakotay (Robert Beltran) and Lt. Paris (Robert Duncan McNeill), who are captured by the time ship.
After a brief interval spent hiding from the time ship in a nebula, Captain Janeway makes an alliance with two species known as the Nihydron and the Mawasi to attack the Krenim timeship. The remaining crew members move to the allied ships while Janeway remains behind alone on Voyager to pilot the heavily damaged ship herself. With the help of a dissatisfied crew member, Chakotay and Paris take the time ship's temporal core offline, rendering it vulnerable to attack, and beam to the nearest allied ship. Even vulnerable and without temporal weaponry, the powerful time ship disables the allied ships. Voyager is badly damaged when one of the ships crashes over the saucer section. Theorizing that the true timeline will be restored if the Krenim ship is destroyed, Janeway orders the fleet to drop their temporal shields and rams Voyager into the time-ship while it is powering up for another temporal incursion. Voyager is destroyed which causes the Krenim time ship's temporal core to destabilize and explode. This erases the time ship from history in a massive temporal incursion thereby resetting the timeline to the day Voyager first encounters the temporal waves.
In the new timeline, Voyager ventures into Krenim space. This time, the captain of the Krenim warship is friendlier - he advises Voyager that this area of space is under dispute and suggests they avoid it. Janeway remarks to Chakotay that she's thinking of replicating a bottle of wine for Voyager's re-dedication ceremony, saying the vintage is a "good year". In this timeline, Annorax is seen working diligently in his study. His wife (Lise Simms) enters and asks him to enjoy the day with her. Annorax hesitates for a moment but decides that he can "make the time" for her. They leave while his work remains behind on his desk, depicting schematics for the Time Ship.