While exploring an uncharted asteroid, Chakotay, Kim and Torres stumble upon what appears to be an alien burial ground. Not wanting to desecrate the site, Chakotay and his team decide to make some quick anthropological observations and then return to Voyager. But before they finish their study, a subspace vacuole — a dimensional distortion — forms and begins to fill the cavern they're investigating. Alarmed, Chakotay orders Voyager to beam them up. But when the Away Team appears on the ship, there is only Chakotay, Torres and the body of a recently deceased woman.

Kim returns to the U.S.S. Voyager from the Banean homeworld with shocking news: Paris has been found guilty of murder. As his punishment, he's been sentenced to relive the crime from his victim's perspective every 14 hours, thanks to memory engrams implanted in his brain by a Banean doctor. Kim recounts how he and Paris were introduced to an engineering physicist named Tolen Ren, who they hoped could help them repair a damaged piece of equipment. Paris took an immediate interest in Ren's young, attractive wife Lidell, and when Ren turned up dead, he was arrested.

When Ensign Kim finds a wormhole that might lead to the Alpha Quadrant, the crew believes they may have found a rapid route home. Although the opening to the tunnel in space proves too small for Voyager to fly through, Janeway decides to launch a microprobe into it to see what's on the other side.

Eager to raise the morale of the crew, Janeway jumps at the chance to explore a nebula emitting a high level of omicron particles, which might prove useful for the ship's energy reserves. But shortly after Voyager enters the cloud-like formation, it encounters an energy barrier that brings the ship to a dead stop. Breaking through, the ship continues its penetration of the nebula's inner reaches, only to be bombarded by peculiar globules that attach themselves to the hull. With the globules beginning to drain the starship's energy reserves, Janeway orders the crew to leave the nebula, but this time they can't get past the energy barrier until they blast their way out with a photon torpedo.

The excitement over, Paris invites Kim to tag along for some rest and recreation in Sandrine's, a holodeck recreation of a French bar that Paris frequented in his Academy days. In the meantime, Torres spends her time analyzing one of the globules that attached itself to the hull. Surprised at the results, she confirms her findings with the Doctor and then notifies the Captain. The globules are organic elements of a much larger lifeform, she explains. In other words, the nebula was actually a living entity and the phenomena they encountered were part of the entity's natural defense systems.

Concerned that the encounter with Voyager may have caused the lifeform serious injury, Janeway proposes returning and repairing the harm they've done. The Doctor tells her that the organic samples seem to indicate that the lifeform has the capacity to regenerate, given the appropriate stimulation.

During an Away Team survey of a planetoid that seems to be rich in raw dilithium, Neelix is attacked and left for dead. The other members of the team find him and beam him up to Sickbay, where the Doctor reports that the Talaxian's lungs have been removed. With no other alternatives, the Doctor fits Neelix with a set of holographic lungs. They'll keep him alive, but require him to remain confined in an isotropic restraint in Sickbay for the rest of his life.

Investigating its origins, the crew finds a nearby planet where a cataclysmic explosion recently wiped out all life. Beaming down, the Away Team discovers that the detonation has actually fractured subspace. But before they can react to this dangerous revelation, Paris and Janeway find themselves transported back in time to the day before the explosion.

Torres is reprimanded by Chakotay after she ends a dispute in engineering by breaking the nose of a Starfleet officer named Carey. But despite her volatile nature, Chakotay has faith in the Klingon woman's skills, and he recommends Torres to Janeway for the position of Chief Engineer. Janeway is surprised, but before she can consider the recommendation, the U.S.S. Voyager is jolted as it enters a region of spatial distortions. A short time later, it comes upon a ship that is trapped in the event horizon of a quantum singularity: the powerful energy field surrounding a collapsed star.

After reaching the Badlands on a search and rescue mission, Voyager encounters an inexplicable phenomenon that sends the ship hurtling to the Delta Quadrant, located 70,000 light years from home. The catapult effect kills a number of crewmembers, including the Chief Medical Officer, who is replaced by an Emergency Medical Hologram (EMH) that attends to the wounded. But the EMH has barely begun his work when the entire crew of Voyager is transported to what appears to be a pastoral farm, populated by friendly humans. But it's only an illusion; the farm is actually the interior of the Array, a huge space station, and the residents are holograms. The crew is imprisoned within a strange laboratory facility, alongside the missing Maquis.

With Chakotay's ship destroyed in the battle with the Kazon, Janeway asks the Maquis to become part of Voyager's crew. She also allows Neelix and Kes to stay aboard. With Chakotay her First Officer, Tom Paris reinstated as a Starfleet lieutenant, and Torres and Kim cured by the Emergency Medical Hologram, Janeway and her new crew set course for the long trip home, 70,000 light-years away.