Voyager enters an area of space that is devoid of stars. The crew is told that it might be two years before they make it to the other side. As time in the void drags on, the crew becomes more and more despondent, and Capt. Janeway secrets herself away in her ready room.
When the ship losses power, and is attacked and boarded, Voyager is rescued by another race's ship. The Malon ship that rescued Voyager has an amazing proposal for the crew. If they turnover the boarding party alien whom they captured during the attack, the Malon will take Voyager through a spatial vortex that they know about, that will take them all the way across the void.
However, the crew learns that the Malon are using the void as a dumping ground, and poisoning the territory of the attacking aliens. The crew must decide if they should destroy the spatial vortex, or take the easy way out.
A transporter malfunction causes the Doctor's mobile emitter to fuse with some of Seven of Nine's Borg implants. When the emitter assimilates a crew member, Seven becomes aware of a Borg presence on Voyager. Worse, the Borg are also alerted to Voyager's presence.
In order to retrieve a probe stuck in a hazardous atmosphere, Tom Paris designs a new type of shuttlecraft named the 'Delta Flyer'. Torres begins to exhibit reckless behavior by engaging in dangerous holodeck programs.
Stardate: 52136.4 Voyager investigates a strange alien structure in space. To their surprise, they find it is a staging point for Species 8472's planed incursion into normal space, and attack on the Federation. They have found a means to take human form, and are training in a recreation of Starfleet Academy.
While Voyager searches for the crew of the crashed Delta Flyer carrying Tuvok, Paris and Ensign Wildman, Neelix must keep Naomi occupied. When it is discovered that Samantha is badly injured, he must decide how much he should tell her daughter.
Voyager uses new quantum slipstream technology in an attempt to get home, but a miscalculation causes the ship to crash into an ice planet. Fifteen years later, the sole survivors, Chakotay and Kim, steal the Delta Flyer in an attempt to send a message back in time and avert the disaster, however, Captain Geordi LaForge is determined to stop them at all costs.
Stardate: 52188.7 Species 6339, as they are known to Seven of Nine, have created a virus designed to attack the Borg. Unfortunately, Voyager finds the delivery vessel, a vinculum, and Seven of Nine becomes infected. This leads to a conflict between Voyager and Species 6339, who want the vinculum back, so it can be used for its original purpose.
When an alien attaches itself to B'Elanna's nervous system, the Doctor enlists the help of a holographic recreation of the Cardassian Dr. Crell Mossett. She refuses all treatment when the Bajoran crew informs her that this doctor was responsible for sadistic war crimes during the occupation.
Stardate: 52179.4 Paris is confined to the brig for thirty days, after he disobeys the Captain's orders and helps to destroy a reactor that may eventually destroy a water world the size of a planet. During his confinement, he recounts what happened in a letter to his father, Admiral Paris.
While travelling through Devore space, Captain Janeway must hide all telepaths on board in transporter stasis as telepathy is illegal under Devore law. After Voyager is repeatedly searched, the leader of the investigations requests asylum and wishes to defect.
The Doctor discovers that his short-term memory has been altered with some events being deleted, so he launches an investigation into whom or what could be responsible. When he sets a trap and the culprit is caught, he is shocked at who it is and why they're doing it.
When Voyager becomes stuck in some sort of gravimetric sandbar, one of Tom Paris' holodeck programs, "The Adventures of Captain Proton", which was running at the time, gets strange alien visitors who exist as holodeck like photons. The villain in Tom's program meets the aliens, and decides to go to war against them. This causes power surges on Voyager. To contact the aliens, the crew must interface with the aliens on the holodeck, meaning they must also face the program's maniacal villain, Dr. Chaotica!
Tuvok and Paris are sucked into a strange gravity well in which all ship that have entered have never left. On the planet they crash on, they meet a mysterious woman, who seems to be smitten with Tuvok.
As Voyager attempts to locate the shuttle, they find another race is intent on destroying this strange gravity well area of space, giving Voyager a limited time to find and rescue their crewmates.
When Voyager finds a miraculous way back to the Alpha Quadrant, Seven of Nine, who has returned from an away mission, questions this fortuitous event. Seven soon learns there is another alien ship nearby whose Captain confirms her fears. He informs her that a great space born beast is feeding on the crew of Voyager, one he is intent on destroying.
Seven must fight the physiological affects the space born beast is having on the crew, while trying to save the ship from destruction.
Stardate: 52619.2 When Voyager encounters, and destroys a Borg Cube, Seven of Nine finds valuable information in the wreckage about another crippled Borg Cube. The crew then decides to tempt fate by attacking the disabled Cube and steal their transwarp drive, in an attempt to shave twenty years off their trip to the Alpha Quadrant.
After defeating a Borg ship, Captain Janeway decides to launch an attack to steal a trans-warp coil to shorten Voyager's journey home. The Borg detect her plan, and access Seven Of Nine's neural transceiver to deliver an ultimatum: re-join the collective or the ship and its crew will be assimilated. If she agrees, the ship will be guaranteed safe passage through Borg space.
Stardate: Unknown Working with a large generational ship that houses the Varro, the crew of Voyager help aid them in their quest to return home faster. At the same time, Ensign Kim becomes involved with one of the Varro and finds himself growing more attached to the woman with each day.
Stardate: 52586.3 Paris and Torres share their wedding vows, but when strange cohesion problems occur on Voyager, it appears things are not what they appear.
Chakotay finds himself in a boxing ring and in a boxing match. However, he soon finds he is moving back and forth in different realities, in Voyager's attempt to communicate with a strange alien race.
In a twist, a space ship "think tank" team, that just happens to be around to save Voyager from several attacking ships, actually has its own secret agenda, which involves recruiting Seven of Nine into their group. But will Seven agree to join them, and if she doesn't, what action will they take?
Voyager responds to a distress call, only to find it's from a Malon ship in distress. They find two survivors in life pods, who speak of a mythical radioactive beast that they believe, caused their ship to become disabled. What Voyager's crew discovers while trying to fix the Malon ship is even more shocking than a mythical monster.
When the Doctor tries to teach Seven of Nine how to date, as part of his attempt to humanize her, he gets caught up in his task, and soon one of the crew learns that the Doctor has become smitten with Seven.
When the senior crew reminisces about their respective ancestors, Capt. Janeway tells about one of her ancestors that became famous working on the first successful self-sustaining enclosed civic environment, the Millennium Gate. However, upon further investigation of this famous ancestor, Shannon O'Donnell, and the Millennium Gate project, Janeway learns some surprising facts about Shannon that causes her to feel less about her hero.
Stardate: 52861.2 Seven of Nine becomes an agent of a time traveling ship from 500 years in Voyager's future, in order to try to prevent the destruction of Voyager, its crew and the effect she is told, it had on the timeline. However, Seven has tried unsuccessfully three times already to find the temporal disruption weapon that caused Voyager's destruction, and each attempt is has a deleterious effect on her health, and she has only a couple of time-trips left, before irreparable harm will occur.
When Seven eventually finds out who has planted the time weapon, she is shocked! However, can she stop the individual in time to save the timeline, and can she do it on this her last possible trip back in time?
Voyager answers a distress call, only to find a bio-neural device imbedded in rock on a planet. Voyager beams the device back to Voyager, but then learns from the Doctor that the device is actually a weapon of mass destruction. Torres must remove the bio-neural mind of the device from the weapon. However, her attempt awakens it, and it then arms itself. Torres then tries to fry the device with an electro-magnetic pulse, only to find the device has taken over the Doctor's program. Now the device / Doctor demands it be taken to its intended target, the home planet its creator's were at war with.
Every attempt to deceive the device fails, and soon Voyager finds itself surrounded by thirty-two more devices. Voyager must now stop all the devices from completing their task, as Voyager's investigation reveals that the devices had been given a recall order, as the war is over; an order the devices refused to accept as being a deception by the enemy.
In a surprising twist, Voyager finds a Federation Starship when answer a distress call. They learn this ship, the Equinox, was also pulled into the Delta Quadrant by the Caretaker. The Equinox is under attack by nucleogenic life forms from an unknown interspatial realm. Voyager extends its shields around both ship, which momentarily protects them both.
In trying to learn why the Equinox was under attack, they learn the Equinox' crew's dark secret, which turns out to be directly related to the interspatial aliens. Worse, they find the ship's Captain will do anything, and sacrifice anyone, to get his people home - even if it means sacrificing Voyager and its crew.