Voyager diverts through a dense nebula to prevent detection from two nearby Vidiian planets. As they exit it, the ship hits subspace-turbulence and suffers from power-failures. B'Elanna Torres prepares to begin a series of photon-bursts to keep the antimatter-reaction in the warp-engines alive; however, Voyager is bombarded with proton bursts from an unknown source. The bursts cause systems to fail across the ship, hull ruptures, and casualties, including the loss of Harry Kim through a hull breach and the newborn Naomi Wildman due to failures in her life-support system. Kes, en route to provide medical attention for the wounded, disappears through a space-time rift. As the crew recovers, Torres discovers there is air on the other side of the rift, and believes that it may be possible to rescue Kes. The bridge crew is forced to evacuate the bridge as it is engulfed in flames, but as she leaves, Captain Kathryn Janeway sees a ghostly image of the bridge-crew, calmly at their stations.
The viewer is then shown the immaculate bridge of Voyager, where that version of Janeway watches a ghostly image of herself evacuate the bridge. This Voyager has not suffered from any ill effects, but is aware of a duplicate Voyager due to Kes's arrival through the rift. The respective crews are able to make contact with each other, and conclude that upon exiting the nebula, Voyager and its crew were duplicated as a result of a space-time rift, creating "quantum doubles". However, this did not replicate the anti-matter, and both ships are suffering from power-losses.
The two crews first attempt to merge the ships, but the effort is unsuccessful. Janeway from the undamaged Voyager crosses through the rift along with the duplicate of Kes. The two Janeways meet to discuss options, recognizing they would not be able to have the entire crew of the damaged Voyager evacuate to the undamaged one without creating a quantum imbalance. Janeway from the damaged Voyager states she will initiate a self-destruct of her ship to allow the undamaged one to regain power. Janeway from the undamaged ship asks her counterpart to delay the start of the self-destruct by 15 minutes to devise another option, and returns to her ship via the rift.
The undamaged Voyager is attacked by Vidiian ships; due to the lack of power, the ship is vulnerable and soon Vidiians appear on board the undamaged Voyager and begin harvesting vital organs from the crew. The damaged Voyager appears to be undetected by the Vidiians. Due to this fact, Janeway from the undamaged ship orders her Kim to collect baby Naomi Wildman and escape into the rift to the damaged Voyager, and then begins a self-destruct of her Voyager; the explosion destroys the ship and the attacking Vidiians, leaving the damaged Voyager free and returning to normal power-reserves. Kim returns Naomi to her mother, and ponders whether this is really his Voyager.