Voyager finds an automated life-form adrift in space. When B'Elanna Torres reactivates it, the unit realizes she may be able to help build more of its kind. The robot kidnaps Torres and gives her an ultimatum: build a working prototype or Voyager will be destroyed.
After finding a type of dilithium which can survive at higher temperatures, Tom Paris comes up with the ingenious idea of attempting to cross the transwarp threshold in an attempt to find a way to get home faster. After a bumpy start and the help of Torres and Kim, they succeed in a holodeck simulation. When it is presented to Captain Janeway, she is impressed and gives them the go ahead to try it, but traveling faster than warp 10 has never before been attempted. The first run goes very well. Tom Paris manages to cross the warp threshold which means that the shuttle ...
Tuvok investigates the murder of a Voyager engineer. Former Maquis and Betazoid Lon Suder confesses to the murder and offers no explanation or signs of remorse. Tuvok, curious to find a reason for Suder's madness, performs a mind-meld on the killer, only to find himself losing his usual Vulcan control and regressing into madness.
Voyager comes across a ship that has been destroyed, upon investigation they discover that B'Elanna Torres is responsible! Dreadnought is a self guided missile created by the Cardassians to destroy the Maquis, however the bomb failed to go off allowing B'Elanna to get inside the missile and re-program it to do the Maquis' bidding.
While Voyager investigates what appears to be a rogue comet, the crew accidentally releases a member of the Q Continuum who has been imprisoned within it for over 300 years to prevent him from committing suicide. He then requests asylum on the ship, which leaves Captain Janeway to decide whether he should go back into confinement or whether to grant his request for asylum, which would give him the opportunity to end his life.
A "spatial scission" causes Voyager to be duplicated. One of the Voyagers is under heavy attack from the Vidiians while the other remains impervious. Both Captain Janeways work together and agree to sacrifice one ship to save the other. Before self-sacrifice, the doomed Voyager sends its version of Ensign Kim and newborn Naomi Wildman to the other ship to replace the Kim that was killed in the attack and the baby who died from complications shortly after birth.
Tuvok and Neelix are on an alien planet collecting examples of flora but when they attempt to beam back up to Voyager there is a malfunction with the transporter caused by the alien plant life they collected causing them to merge together as one life form, 'Tuvix'.
Almost the entire crew of Voyager have been marooned on a desolate planet by the Kazon. Tom Paris was sent out to try and find someone who can help them. Furthermore, Lon Suder and the Doctor, who are still on Voyager, try to help.
Captain Janeway participates in a mind meld with Tuvok, who relives his experiences on the U.S.S. Excelsior under the command of Captain Sulu at the time of Star Trek VI: The Undiscovered Country (1991).
Tom Paris and Harry Kim are wrongly convicted of a terrorist bombing. Even though Janeway captures the true criminals, Tom and Harry are fitted with strange brain implants and imprisoned on a satellite. In the prison, the inmates have no supervision, no medical care, and all have implants which increase their aggressive tendencies. New prisoners and food-rations are delivered through a one-way chute. As days pass, the friends try to hold on to reality but find themselves turning on one another and taking drastic measures to survive and attempt escape.
Voyager is attacked by swarms of tiny spaceships which attach themselves to Voyager's hull. The Doctor is losing his memory and Torres activates the Jupiter Station diagnostic program run by a familiar hologram.
A timeship from the future who tries to stop Voyager gets thrown with Voyager into the twentieth century. His timeship is found in the 1960's and Voyager finds a company that has benefited from its technology exists in 1996.
Henry Starling, who made a fortune from his looting of 29th century technology from the crashed timeship, is planning a foray into the future to feed his greed. The Voyager crew must find a way to stop Starling before his attempted use of the timeship destroys Earth's Solar System. Meanwhile, while trying to rescue Paris and Tuvok, Torres and Chakotay are captured by an anti-government white supremacist militia who believe that they are feds.
Due to the death of the Q in their last encounter with Voyager, a Civil War has broken out among the Q continuum. A new Q needs to be produced and the mischievous Q known to the USS Enterprise has chosen Janeway as his mate.