Badly damaged, the U.S.S. Voyager takes refuge in a nebula, as a skeleton crew attempts to repair the ship. On Annorax's ship, Chakotay and Paris are summoned to meet with him. He has a proposal for them. He'll send Voyager back in time, restoring it to its original state, if they fill him in on the extent of Voyager's presence in Krenim space so he can complete calculations that will allow him to restore the Krenim Imperium. Paris balks at helping Annorax, but Chakotay believes the chance to continue their voyage home may be worth the risk of trusting Annorax.
As Chakotay helps Annorax chart Voyager's journey, Annorax shares a story about a mistake he made after he first created his time-weapon ship. He destroyed the Krenim's greatest enemy, but in the process, he also destroyed an important antibody in the Krenim genetic structure, and 50 million Krenim died of disease as a result. He has been trying to undo his mistake ever since.
Paris finds a weakness in the Krenim ship that could be exploited, but Chakotay refuses to go against Annorax. However, when Annorax eradicates another species in order to partially restore the Krenim timeline, Chakotay is dismayed to see him turn once again to destruction as an answer to his problems. Chakotay takes Annorax to task for the destruction of innocent lives and Annorax reveals the driving force behind his actions. His wife died as a result of his time incursions, and he hopes to undo her death.
Chakotay and Paris secretly contact Voyager, giving Janeway their coordinates. She arranges a coalition with other species, which will attack when Paris takes the temporal core off-line. The remaining members of Voyager's crew disperse to prepare the other ships for battle, but Janeway stays with Voyager.
Chakotay and Paris take the temporal core off-line, making the ship vulnerable to traditional weapons. Annorax orders his men to fire at the approaching vessels and soon the coalition is almost destroyed. Janeway does a kamikaze run at the Krenim ship and the impact destabilizes the core, causing a temporal incursion within Annorax's ship. With the destruction of the Krenim vessel, the timeline is restored, Voyager never makes its fateful entry into Krenim space, and Annorax is at last reunited with his beloved wife.