Upon encountering a pair of planets inhabited by Vidiians, Voyager diverts to take a path through a dense nebula, to prevent detection. However, upon reaching the other side of the nebula, the ship hits subspace turbulence and sustains power failure. Antimatter is being drained, and B'Elanna concludes proton bursts could keep the antimatter reaction going. Samantha Wildman's baby, a half-Ktarian girl, is delivered by transporter owing to complications. Before the proton bursts are initialised, a mysterious proton bombardment causes serious damage on board Voyager. The loss of power interrupts lifesaving treatment to stabilize newborn Naomi Wildman's cell membranes and she dies. The proton bursts also cause heavy crew casualties. Harry Kim is blown into space and Hogan is injured in an attempt to repair a hull breach.
En route to treat Hogan, Kes inadvertently runs through an invisible rift in space-time. B'Elanna establishes that there is air on the other side of the rift, so they assume that Kes may still be alive. Meanwhile the Bridge is engulfed in flames and the crew has to evacuate. As Janeway escapes she sees what appears to be a ghostly image of herself and her crew, still at their posts.
The scene switches to the Bridge, this time undamaged. Janeway catches a glimpse of her injured self fleeing the flames. Suspecting spatial anomalies, she asks Harry to initiate a scan because she's just seen herself "looking like hell."
In Sickbay, the Doctor is seen happily treating Sam and her baby Naomi, both of whom are perfectly healthy. Kes is there. When she wakes up she explains that she is from another "version" of Voyager and she got here through the space-time rift. The crew realize that the ship has been duplicated, still occupying the same position in space, during the proton bombardment. The duplication created quantum doubles of all of the matter on board, but not the anti-matter, hence there is a severe drain as both ships draw on the same source. Janeway decides to try to contact the other ship.
B'Elanna and Janeway work together to make contact, but they are unable to merge the two ships. Janeway decides to visit the damaged ship. She is accompanied by the Kes from the duplicate ship, who knows she will be needed in Sickbay.
The two Janeways meet and discuss their options. They cannot transfer both crews to one ship because this will create an imbalance. The undamaged Janeway correctly intuits that her counterpart will self destruct the duplicate Voyager "because it's what I would do". She then returns to her own ship.
Before any action can be taken Vidiians appear and attack the duplicated, undamaged Voyager. Without weapons and shields, Voyager is quickly overrun and the Vidiians storm the ship and kill crew members for use as spare parts. The damaged, original Voyager remains undetected.
On the duplicated ship, Janeway orders Harry to Sickbay to collect the baby and take her to safety on the original ship. The Vidiians reach the bridge in time to see the self destruct timer count down from 5 seconds, destroying the duplicated Voyager and the Vidiian ship.
Harry makes it to the original Voyager and places the baby safely in her mother's arms.