Crew morale hits an all-time low when Voyager must spend two years crossing an expanse devoid of any star systems or signs of life. As Captain Janeway is forced to reflect on the choice she made stranding her crew in the Delta Quadrant, little does she know, she will face a similar decision when Voyager ends up in the middle of a serious conflict.
Voyager is investigating the birth of a nebula. Unfortunately, after an away mission shuttle is caught in the blast, a transporter accident during the team evacuation causes the Doctor's mobile emitter to be infected with Seven's nanoprobes. The mobile emitter starts assimilating a science lab, and creates a new drone built upon the emitter's twenty-ninth century technology.
B'Elanna Torres secretly participates in several dangerous holodeck programs. The Voyager crew works around the clock to build the Delta Flyer, hoping to beat the Malon in retrieving a lost probe from the atmosphere of a gas giant.
The crew of Voyager discover a simulation of Starfleet Headquarters being run by Species 8472. With the aid of regular doses of drugs, Species 8472 are able to shape-shift into human form. It is up to Janeway to try to convince the aliens that Starfleet is not a threat to them.
The Delta Flyer crash lands after encountering an ion storm. Voyager desperately tries to contact and rescue Tuvok, Paris, and a badly injured Ensign Samantha Wildman. Meanwhile aboard ship, Neelix attempts to distract young Naomi Wildman, who is eager to hear from her mother. Finding out the truth, Naomi escapes into a popular children's holo-novel.
A miscalculation by Ensign Kim causes a fatal crash during Voyager's first test with slipstream travel. Fifteen years in the future, survivors Chakotay, Kim and The Doctor attempt to send a message back in time to prevent the tragedy.
An injured cytoplasmic life-form attaches itself to Torres, tapping into her body like a parasite. Unsure of how to save his patient, The Doctor creates a holographic recreation of a non-humanoid exobiology specialist to consult the case. The consult is going well until Torres refuses treatment when it is made known the Cardassian specialist was responsible for tortuous experiments resulting in the deaths of thousands of Bajorans.
Voyager passes through a sector of space controlled by race which is deeply suspicious of telepathic lifeforms. Tuvok and others force the Voyager crew to develop a novel approach in order to pass through safely.
The Doctor uncovers evidence his memory was erased 18 months ago. Nearly all traces of a crewman and a fateful away mission have been deleted by Captain Janeway. Confronted by The Doctor's need for answers and Seven of Nine's perspective on the rights of a hologram, Janeway restores the fatal truth about Ensign Jetal, The Doctor's choice that led to her death, and his resulting breakdown.
While Tom Paris and Harry Kim are running an episode of their "Captain Proton" holodeck programs, Voyager gets caught in a layer of subspace. However, this layer or 'subspace sand bar' as it is nicknamed is home to a race of photonic aliens. There is one big problem: they are not able to detect Voyager or any carbon based life forms (humans). Instead they transport down on to the holodeck and start a war with Dr. Chaotica's Army of Evil. When Voyager detects internal weapons fire on the holodeck, Tom Paris and Tuvok are dispatched to find out what the problem is. When...
A Voyager shuttle manned by Lt. Cmdr. Tuvok, Ensign Paris and The Doctor is pulled into a subspace gravity well and crashes on a Class "D" planet existing within it. With the shuttle too damaged to fly, the away team befriends Noss (guest star Lori Petty,) an alien woman who crashed on the planet several seasons before them. As weeks pass, the survivors grow close. Noss learns English and teaches Tuvok and Paris how to survive the other aliens and hunt for food. Noss finds herself in love with Tuvok, and frustrated that he will not allow his emotions to love her back....
The Voyager crew discovers what seems to be a wormhole leading to the Alpha Quadrant and home. Images of Earth and letters from home elates the crew of Voyager. Seven, and others, however, are skeptical of this seeming deliverance.
Members of the Voyager crew train on the holodeck for a raid on a Borg ship. Should they be successful, they will steal the Borg trans-warp coil in hopes of integrating the technology into Voyager's systems. The Borg seem to be one step ahead when the Borg Queen communicates with Seven of Nine.
Janeway is confused but won't give up on her crewmate and friend. Two years after being liberated from the collective, Seven of Nine rejoins the Borg, seemingly of her own will. When Janeway finds a history of transmissions from the Borg to Seven, she is convinced that Seven was lured back against her wishes. Meanwhile, aboard the Borg sphere, the Borg Queen attempts to seduce Seven into helping her assimilate Earth.
Voyager encounters a group of xenophobic nomads, in space for 400 years, with serious ship wide malfunctions. This offer to help leads to serious consequences. Straitlaced Ensign Kim gets entangled in a forbidden romance.
Voyager gets trapped in "chaotic space," a kind of Bermuda Triangle, where sensors are useless and a straight line sends them running in circles. In an attempt to relay to Voyager that they are not welcome, the inhabitants of chaotic space activate a genetic defect in Commander Chakotay, who interprets the warnings and instructions in the form of hallucinations including his Grandfather and his boxing training at Starfleet Academy.
Voyager is sought after by the Hazari, unyielding bounty hunters of the delta-quadrant. While debating methods of escape, a group of problem-solvers offers their services in out-witting the Hazari. The group spokesman Kurros (guest star Jason Alexander) proposes a payment method to Janeway: one of Neelix's famed recipes, an artifact owned by Chakotay, and Seven of Nine herself.
Voyager responds to a distress call of a heavily-damaged Malon freighter. Torres, Neelix, Chakotay, and the only 2 surviving Malon have 6 hours to stop a theta-radiation fallout which will destroy everything within a 3 light-year radius. The away-team must clear radiation section-by-section to reach the control room, and along the way they deal with unstable airlocks and the Vihaar, a Malon boogeyman who is more malicious than mythical.
Voyager makes first contact with the Kadi, a ritualistic race with many social protocol. Seven takes the advice of the Captain and The Doctor gives her classes in dating. Neelix plays babysit-the-drunk when Tomin (guest star Scott Thompson,) the Kadi Ambassador turns from preacher to party animal. The Doctor finds himself falling for his student.
The crew of Voyager swap stories of family histories. Janeway is most proud of her ancestor Shannon O'Donnell, who has been celebrated by the Janeway clan for generations as an astronaut and pivotal member of The Millenium Gate and several Mars projects that followed. When research and history-buff Tom Paris prove the stories wrong, that O'Donnell wasn't the hero Janeway made her out to be, the crew points out that her inspiration made Janeway join Starfleet and that is an accomplishment in itself.
When Voyager is destroyed, Captain Braxton of the 29th Century Timeship Relativity contacts Seven of Nine to travel back in time and discover who planted the 'temporal disruptor.' However, she must do this without being discovered by the past Janeway.
Voyager encounters the Federation Starship Equinox, a Starfleet vessel trapped in the Delta Quadrant by the same alien who brought Voyager there. Equinox is heavily damaged and running with a skeleton crew. Happy to have found each other, Voyager assists Equinox in fighting off an non-humanoid alien race attacking them. But Equinox has earned the aliens hostility. Captain Ransom and his crew have been kidnapping and killing the aliens and using their unique physiology to enhance their warp drive. When Janeway imprisons the Equinox crew they stage a revolt. The Equinox...