A means of direct communication is established with Voyager allowing each crew member to speak with family and friends. The Doctor sends a holo-novel for publication based on a lost starship with a doctor who is treated like a slave, which causes controversy among the members of the ship.
Under attack by the territorial Turei, Voyager sets down on an uninhabited planet to hide and make repairs. In a cavern under the surface, they discover and revive the final remaining survivors of the Vaadwaur, the planet's original civilization, who had been in stasis for nearly 900 years. As Voyager and their new allies prepare to engage the Turei, there is reason to fear that the Vaadwaur are more dangerous than originally suspected.
During a near-death experience, B'Elanna finds herself aboard the Klingon Death Barge, a spectral vessel which transports dishonored souls to Grethor. After seeing her mother there, B'Elanna risks her life to go back and save her mother's soul from this fate, even at the cost of her own.
Captain Janeway relates the story of her distant ancestor, Shannon O'Donnell (Kate Mulgrew in a dual role), and her involvement in the construction of Earth's "Millennium Gate". She meets and falls in love with Henry Janeway - the one man standing in the way of the Gate's construction.
When an alien attaches itself to B'Elanna's nervous system, the Doctor enlists the help of a holographic recreation of an expert. However, when B'Elanna learns that the expert is a Cardassian that performed immoral medical experiments during the occupation, she refuses treatment.
Voyager is forced out of warp by the detection of a dangerous and powerful particle, called "Omega", that has the power to join subspace. Janeway must enlist the help of the senior staff to carry out a secret standing order from Starfleet - destroy Omega by any means necessary.
While Seven of Nine struggles with her humanity, Captain Janeway tries to help a group of aliens whose species was almost entirely assimilated by the Borg. Meanwhile, the Klingon "Day of Honor" turns into a string of bad luck for B'Elanna.
The Doctor decides he should create a holographic family in order to expand himself. When B'Elanna is disgusted by its unrealistic perfectionism, she alters the program to include random events and outcomes with interesting and devastating results.
In order to stop attacks from the Kazon, Captain Janeway finds herself being forced to make an alliance with the more powerful Kazon sects. When negotiations fail, their only chance is to ally themselves with the race that used the Kazons as slaves in the past, called the Trabe.
After discovering a 1936 Ford truck floating in space, Voyager follows an AM-band SOS call to a nearby planet. There, they discover a series of cryo-stasis chambers containing humans abducted from Earth during the 1930s, including Amelia Earhart and her navigator.
The discovery of a micro-wormhole leading to the Alpha Quadrant allows the crew to communicate with a skeptical and paranoid Romulan. The crew is elated when they believe they might be able to transport to the Romulan ship. However, all is not as it seems.
While in pursuit of a Maquis ship in a region of space known as the Badlands, the starship Voyager, under the command of Captain Kathryn Janeway, is transported 70,000 light years from home into the uncharted region of the galaxy known as the Delta Quadrant.