As Voyager starts its way back home from the Delta Quadrant, tensions between the Starfleet and the Maquis crewmembers begin to rise, and some brief hostilities are incurred. However, both Captain Kathryn Janeway and her first officer, Chakotay, originally the captain of the Maquis crew, agree they need to integrate the two crews as one to fill vacancies left by the disastrous events to date. Of note, Chakotay recommends B'Elanna Torres, one of the more outspoken Maquis and a former Starfleet officer, to be Chief of Engineering, a move that Janeway is hesitant about, considering that Torres recently broke another engineer's nose in a fight.
As the ship passes near a quantum singularity, the Voyager crew detect a ship stuck in the singularity's event horizon. Receiving no contact with the ship, they attempt to move in closer to engage the ship via tractor beams, but the result damages more of Voyager's systems. Janeway orders the crew to take Voyager to a nearby planet to seek help for the trapped ship. However, after some time has passed, the crew finds themselves back at the singularities, and quickly realize the ship they are seeing is themselves from before. The ship has become trapped in the singularity, and it is impacting several of the ship's systems.
Eventually, they discover a point in space where Voyager crossed into the singularity, but it has since shrunk, too small for Voyager to exit through. Janeway takes Torres, who has knowledge of singularities, on a shuttle to the opening, using the shuttle's shields to expand the opening large enough for Voyager to pass through. However, the result damages their communications systems; on returning to Voyager they find two versions of the ship, both appearing real to their sensors. Though they have a heated argument about which ship is the correct Voyager, Janeway makes the ultimate decision, and correctly picks the right vessel. Voyager leaves the singularity safely and begins to affect repairs. Janeway follows through on Chakotay's advice and promotes Torres to Chief Engineer.