Stardate: 48439.7. As the Maquis crewmembers begin to integrate themselves into the Starfleet crew, Voyager becomes trapped in a quantum singularity.

Stardate: 48532.4. During an away mission, Neelix is attacked and his lungs are surgically removed. His only hope for survival is if the crew of Voyager can get them back.

Stardate: 48623.5. A transporter accident swaps Harry Kim with a dying woman from another dimension. Harry finds himself among aliens who believe he’s returned from their afterlife, while the woman, expecting paradise, wakes up on the Voyager.

Stardate: 48642.5. The Voyager crew are offered luxurious shore leave by the advanced and gregarious Sikarians, who have a device that could send Voyager 40,000 light years closer to home. However, Sikarian law strictly prohibits sharing their technology with others.

Stardate: 48658.2. When stolen Federation technology is found on a severely damaged Kazon Nistrim ship, Seska becomes the prime suspect. The evidence is further reinforced when questions arise regarding her true heritage.

Stardate: Unknown. After the Kazon steal some Federation technology Chakotay goes after them on his own and is captured.

Stardate: Unknown. Janeway tries to make an alliance with a Kazon sect for their own protection and so they can continue their journey through the Delta Quadrant.

Stardate: 46504.3. After receiving a Vidiian patient who is about to die from the Phage, the doctor transfers her consciousness into the ship's computer and creates a holographic body. He soon finds himself becoming deeply attracted to her.

Stardate: 49485.2. After weeks of erratic behavior, Tom Paris leaves Voyager and joins a Talaxian convoy.

Stardate: Unknown. Voyager receives a distress signal from Seska, who claims that Maje Cullah is going to take her baby away from her, a baby she says is Chakotay's. Chakotay is skeptical, but can't take the risk of abandoning his child, should it really prove to be his. Janeway authorises a mission to rescue Chakotay's child and the ship moves deep into Kazon Nistrim territory. However: was Seska for real, or is this all an elaborate trap?

Stardate: 50023.4. Voyager is captured by the Kazon and the crew are dumped on a planet in its early stages of evolution. As only Tom Paris and Lon Suder have evaded capture, it's up to them and the EMH to come up with a plan to retake the ship.

Stardate: 50953.4. B'Elanna Torres discovers a holodeck program where Chakotay and the Maquis rebel against Janeway.

Stardate: Unknown - A spatial anomaly divides Voyager into various time frames of the past and future, leaving Chakotay as the only person who may be able to put the pieces back together.