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

Stardate: 48546.2. Janeway tries to figure out what her dynamic with the crew should be while all stuck in the Delta Quadrant together. Voyager tries to harvest omicron particles to refuel the ship, but inadvertently injures a spacefaring organism.

Stardate: 48579.4. The discovery of a wormhole leading to the Alpha Quadrant elates the crew, however, their only contact within range is a skeptical and paranoid Romulan.

Stardate: 49164.8. The crew of Voyager make contact with the Caretaker's mate, Suspiria, and a community of Ocampa that have been living on her Array. One of the Ocampa begins to train Kes in growing her psychic abilities, but pushes her to become more powerful than she can control.

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: 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: Unknown. After returning from a first contact mission, Janeway, Neelix and the Doctor must retake Voyager from an infestation of microorganisms that grow to an alarming size.

Stardate: 51268.4. The Voyager crew finds its determination and morale challenged when trying to survive a brutal, long-lasting conflict with a race called the Krenim.

Stardate: Unknown. Kes returns to Voyager in a state of rage, blaming Captain Janeway for her past. Using her expanded Ocampan powers in a fit of revenge, she travels through time to deliver the crew to the Vidiians.