Stardate: 48623.5 While investigating an asteroid belt containing a new element, Harry Kim is pulled into a 'subspace vacuole' and switched with a dead body. Soon after the body is revived the crew learn that the asteroid belt is the graveyard of an alien culture that transports its dead in the belief that they evolve into a higher state of consciousness. Harry's appearance on the homeworld begins to raise questions about the existence of their afterlife.
Stardate: 48892.1 When the Doctor is activated during a Red Alert, he learns that the ship has been abandoned, and that only B'Elanna Torres and an injured Captain Janeway are left on board. Soon afterwards, Lt. Barclay appears and tells him that his entire time on Voyager is an elaborate simulation, and he's really a holo-engineer by the name of Zimmerman on Jupiter station in the Alpha Quadrant, who has been trapped on a holodeck for six hours. If he does not destroy Voyager's warp core and end the program soon he will die.
Stardate: 49164.8 The crew of Voyager make contact with the Caretaker's mate, Suspiria. Kes meets with the descendants of other Ocampa on Suspiria's array that left the homeworld over 300 years ago. Soon, her mental abilities begin to grow to a point where she can no longer control them, and nearly kills Tuvok in the process.
Stardate: 49690.1 When Captain Janeway and Chakotay contract an incurable virus they are left on a planet that shield them from its effects. While Janeway searches for a cure, she begins to form a deeper relationship with her first officer. Onboard Voyager, Tuvok, who is now in command, faces a near mutiny.
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: 50384.2 Voyager encounters several supernova in a small region of space. Time soon reveals that it is the after effects of a civil war within the Q-Continuum. Q appears and believes that the solution to the problem is for him to produce a child, and his mate of choice is Captain Kathryn Janeway. Matters are complicated when a jealous female Q appears claiming that Q was her boyfriend.
Stardate: Unknown Voyager encounters a region of space named the Nekrit Expanse. Since Neelix has no knowledge about the space after this point, he tries to make himself feel useful to the crew by trying to obtain a map from an old friend named Wixiban, who uses him as a courier for illegal substances.
Stardate: 50693.2 When the doctor tries to improve his personality by incorporating the psychological profiles of famous and historical people, he is overwhelmed by their dark sides and begins exhibiting signs of a split personality, one the regular doctor, and the other dark and evil. Kes asks to leave Voyager when they encounter a race with vast knowledge of the region of space they are currently exploring.
Stardate: Unknown An alien paleontologist discovers a common ancestral link between his people and humans. He believes that this proves that his people (the Voth) evolved on Earth and migrated to the Delta Quadrant millions of years ago, but his government is not as willing to believe his interpretation of the evidence.
Stardate: 51003.7 - The crew of Voyager come up with a solution to the Borg's problem, and are willing to share it with them if they grant safe passage to the ship and its crew. In order to help with the negotiations, the Borg send over a drone designated Seven of Nine as a representative of the collective.
Stardate: Unknown - When B'Elanna faces the Klingon Day of Honor she must retrieve the warp core with Tom Paris, which Voyager had ejected. When the shuttle is attacked, B'Elanna and Tom are left floating adrift in space in environmental suits. Believing they are about to die, B'Elanna does the only honorable thing she can do, and reveals her true feelings towards Tom.
Stardate: 51425.4 - With most of the crew having abandoned Voyager and only a skeleton crew remaining, the crew realize that to stop the Krenim ship from altering history any further, they need allies. They soon realize that the price of history is higher than any of them could have possibly imagined.
Stardate: 51501.4 - Voyager starts receiving messages from Starfleet through the communications network, now that they know that the crew is alive in the Delta Quadrant. Some bad news is received by some of the crew, particularly Captain Janeway among others. After a short while, the messages become lodged in one of the modules, and the crew must retrieve them. Shortly, they are crudely introduced to a new enemy, the Hirogen, who seek nothing more than to kill victims for the thrill of the hunt, and Voyager is their next target.
Stardate: 51652.3 - When Voyager encounters a disabled Hirogen ship with a wounded Hirogen aboard, Captain Janeway beams him aboard. Soon, the prey being hunted by this particular Hirogen, a member of Species 8472, boards the ship. The only immediate solution is to let the Hirogen loose on the ship to attack it prey.
Stardate: Unknown - When the Hirogen capture and board Voyager they discover that the holodeck can be used to improve the hunt by putting the prey through different situations and locations. In one situation, Captain Janeway, Torres, Tuvok and Seven of Nine are members of the French resistance in occupied France with the Hirogen in roles as Nazi SS Officers. Since the crew was implanted with subdermal transmitters, they have no idea that this is on the holodeck, and they think it's real. It is up to the Doctor in sickbay who is forced to heal the injured to disable the devices and help the crew escape.
Stardate: 51781.2 - Voyager is forced out of warp by the detection of a dangerous and powerful particle called 'Omega' which only Janeway and Seven of Nine know about on board the ship. Due to the nature of the particle, only Starfleet Captains are informed and are ordered to destroy it at all costs, as it has the power to destroy subspace. Janeway must enlist the help of the senior crew on a need-to-know basis in order to destroy it safely.
Stardate: Unknown - In search of the vital chemical deuterium essential to Voyager's energy supplies, they discover a 'Demon' planet with reserves large enough to replenish the ship. Ensign Kim and Tom Paris take a shuttlecraft down to the planet's surface in environmental suits. Soon they are found on the planet with no suits, and the ship's atmosphere becomes poisonous to them.
Stardate: 51929.3 - When Voyager encounters a deadly radioactive nebula, Captain Janeway decides to save time by going through it and placing the crew in protective stasis with only Seven of Nine and the Doctor left to protect the ship. Seven soon starts experiencing hallucinations when an alien wants to trade vital supplies.
Stardate: 51978.2 - An alien translator by the name of Arturis is able to finally decode the Starfleet message received by Voyager five months ago. It tells them to go to a new type of ship waiting for them with an engine system faster than warp drive, which is capable of bringing them home within three months.
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.
The ship is placed in danger when it comes under attack from a territorial race of aliens known as the Turei. While sheltering on a planet, Captain Janeway tries to make an alliance with its inhabitants, the Vaadwaur. However, she soon begins to think that the Vaadwaur may pose a bigger threat than the enemy above.
As the crew enjoys time off in a holo-program created by Tom Paris, and set in an Irish village named 'Fair Haven,' Captain Janeway falls for a handsome holo-character specifically designed for her. A deadly neutrino wave approaching Voyager shortly bring the festivities to a halt as this wave may prove to be more dangerous than they first imagined.
Ensign Lindsay Ballard returns to Voyager after being killed during a previous away mission. An alien race known as the Kobali, whose only method of reproduction is 'resurrection' of the dead through genetic engineering had revived her and taken her as a new member of their race. When the full extent of her new Kobali genes are activated, they reach a point where she must choose between her old home on the ship, or her new home with her adoptive Kobali family.
News reaches Voyager through the up-and-running Pathfinder project that the Doctor's creator, Lewis Zimmerman, is critically ill. In an attempt to save his life, the Doctor's program is transmitted to the Alpha Quadrant, but once there, he finds Zimmerman does not want to be examined by an 'obsolete' EMH program.
Seven of Nine is led to a place known as Unimatrix Zero; a place where Borg drones are individuals for a short period of time during their regeneration. However, once their regeneration is complete, all recollection of the event is erased. Captain Janeway uses this to form a plan of attack that would create a mutiny from within the Collective.
Stardate: 54129.4 - Rebi and Azan are reunited with their home worlds, and leave the crew of Voyager. Mezoti is offered the chance to stay with Rebi and Azan, and accepts their invitations to live with them. Seven of Nine is placed in a life-threatening situation when her Borg implants begin to malfunction. The only way she can survive is if they can find replacement parts from a living drone. With Icheb now the last of the remaining Borg children on the ship, he volunteers to offer his implants through a risky procedure that may cost both of their lives.
Stardate: 54058.6 - Paris and Kim volunteer to enter a race that symbolises a peace treaty between four warring races. However, the race's peaceful intentions are undermined with plans of sabotage and murder. Torres feels she is nearing the end of her relationship with Paris. However, they work things out with surprising results.
Stardate: 54283.3 - While in the Delta Flyer, the Doctor, Harry Kim and Seven of Nine come under attack for transporting a hologram through Lokirrim space - an act which is strictly forbidden. To hide the doctor, Seven of Nine downloads him into her cybernetic implants shortly before they are taken to a Lokirrim holding cell. On board Voyager, Tuvok enters Pon Farr.
Stardate: 54274.7 - While Voyager stops for maintenance, Harry Kim, Seven and Neelix use the Delta Flyer to search for dilithium, when they come across a war between two alien races. After receiving a distress call from a damaged ship claiming to be on a humanitarian mission, Harry is offered his first chance at commanding a vessel of his own.
After Voyager passes near a spatial rift, Chakotay is injured in Engineering, leaving his body in a state of temporal flux. After receiving treatment in sickbay, he inadvertently gains the ability to pass through rifts in time that are scattered throughout the ship, enabling him to walk into different stages of Voyager's history over the past seven years.
Stardate: 54584.3 - The crew of Voyager carry out their normal lives as workers on an industrial planet called Quarra, totally unaware of their time on Voyager or their situation in the Delta Quadrant. Chakotay, Kim and Neelix, return from their trading mission on the Delta Flyer to find the ship abandoned and adrift in a nebula, with only the Doctor on board. The Doctor informs them that the ship fell into a trap which forced them to abandon ship in the escape pods, allowing them to be captured. The Doctor has heard nothing from them since. After going undercover on the planet, Chakotay, Kim, Neelix and the Doctor must now find a way to return the crew and restore their memories, while evading local authorities who have uncovered their plan.
Stardate: 54732.3 - A means of direct communication is established with Voyager allowing each crew member to speak with family and friends. The Doctor sends a holo-novel for publication based on a lost starship with a doctor who is treated like a slave, which causes controversy among the members of the ship.
Stardate: 54775.4 - With regular communications to the Alpha Quadrant established, Starfleet send a mission to Voyager: retrieve a 21st Century probe sent from Earth called 'Friendship One.' However, the probe has been modified by a Delta Quadrant species, and the changes may not have been for the better.
Stardate: 54868.6 - When Voyager discovers a settlement of Talaxians on an asteroid caught in an industrial conflict, the crew manage find a new home for the population. When an armed conflict between the mining operations and the re-settled Talaxians erupts, Neelix is offered a chance of a new life away from Voyager within the colony.