The U.S.S. Voyager is fired upon by the 29th-century Federation "Timeship" Aeon commanded by Captain Braxton, who has time-traveled through a spatial rift to destroy Janeway`s ship. Braxton claims that Voyager is responsible for a temporal explosion that will obliterate Earth`s solar system in his era.
Janeway`s attempts to beam up 20th-century computer mogul Henry Starling and the timeship in his possession are stymied because Voyager`s long-range transporters aren`t working. As a result, brilliant astronomer Rain Robinson lures Starling to a meeting where the crew hopes to hijack him.
The U.S.S. Voyager beams aboard three people just before their damaged ship explodes. Although the Doctor and Kes try to save him, Tieran dies. When Voyager arrives at Ilari, the local leader, sends a representative to the ship. Inexplicably, Kes pulls out a phaser, kills the representative and a crewmember.
Preparing for an Away Team mission to a planet with a large reserve of gallicite, Torres is taken aback when a Vulcan ensign named Vorik asks her to be his mate. She declines, but Vorik grabs hold of her face and she dislocates his jaw.
Returning from a scouting mission, the shuttle manned by Chakotay and Ensign Kaplan picks up a Federation distress call from a planet. Launching a buoy to let Voyager know where they are, they land the craft, but are quickly attacked by a hostile group of humanoids.
During an encounter between the U.S.S. Voyager and a Nasari ship, Kim announces that the alien ship is going to fire, and he unleashes Voyager`s phasers at it, triggering an unwanted battle. As both ships limp away from the confrontation, Janeway grills Kim, who says he just "knew" the Nasari posed a threat, despite their non-aggressive behavior.
After Janeway and Paris leave on an away mission, Chakotay leads a Maquis takeover of Voyager. With Torres` help, he seizes control of the ship and vows that Federation principles will no longer stand in the way of getting the crew home.
Realizing they have entered Borg space, the crew attempts to plot a course through a corridor that seems devoid of Borg activity, which they dub "the Northwest Passage." As the Doctor and Kes research methods of fighting off Borg assimilation, Kes is troubled by recurring visions of dead Borg and the destruction of Voyager.