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 in the search for dilithium crystals, Neelix is attacked and his lungs are surgically removed by a disease-ridden race of aliens known as the Vidiians. His only hope for survival is if the crew of Voyager can get them back.

Stardate: 48623.5. While investigating an asteroid belt containing a new element, Harry Kim is pulled into a 'subspace vacuole' and switched with a dead body. Soon after the body is revived the crew learn that the asteroid belt is the graveyard of an alien culture that transports its dead in the belief that they evolve into a higher state of consciousness. Harry's appearance on the homeworld begins to raise questions about the existence of their afterlife.

Stardate: 48642.5. Harry Kim discovers advanced technology when a race of aliens known as the Sikarans offer shore leave to the crew of Voyager. This would send Voyager 40,000 light years closer to home, however, the Sikarians' "Canon of Laws" forbids them from sharing their technology with anyone.

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.