Voyager follows a trail of spaceborne rust, where the crew finds a centuries-old land vehicle from Earth drifting through space. When Paris manages to start the old truck, Harry's curiosity about its AM radio uncovers an equally ancient S.O.S. coming from a nearby planet. Janeway, hoping that whatever brought the truck and the source of the distress call to the Delta Quadrant could be found and used to send Voyager home, orders a landing. A vintage airplane is found on the surface with an alien power supply keeping the S.O.S. on the air, and eight alien-abducted humans are found in stasis chambers also constructed by an alien intelligence. The 20th century humans are revived, and Janeway finds that among them is the long-lost pioneer female aviator Amelia Earhart.
Alone in a shuttlecraft preforming the Pakra, a solitary ritual commemorating his father, Chakotay is attacked by a Kazon-Ogla vessel. When he destroys the attacking craft and rescues the lone pilot, he discovers that his opponent is a young boy trying to make his mark in Kazon society by killing an enemy; the price of the boy's failure is ostracism from his culture. Chakotay is faced with the dilemma of saving his own life while righting the harm he has unwittingly done to the boy.
Automatically brought online by a red alert, the doctor finds that the ship has - according to the computer - been abandoned after a Kazon attack. But this turns out to be wrong when Torres shows up to enlist the doctor's help in aiding the injured Janeway on the bridge. Thanks to a holographic projection system that can transfer the doctor to key parts of the ship other than sick bay, he can help people all over the ship. But then the doctor's grip on reality is loosened when he finds that not only can he bleed, but according to every available tricorder he is the only living thing on board Voyager.
A strange energy disturbance detected by the crew turns out to be a swarm of space-dwelling life forms whose electrophoretic emissions cause sudden hormonal maturation in Kes. She spontaneously enters the Elogium in preparation to have a child, which she desperately wants. Neelix is troubled by the thought of becoming a father and seeks the advice of Tuvok. Kes' condition causes Janeway to wonder about the implications of raising families aboard Voyager, but the crew's immediate concern is the dominant member of the swarm, which views the ship as a rival for mates.
Harry Kim wakes up in San Francisco where he finds himself in bed with his fiancee. He is a bright young Starfleet engineer, and his friend Ensign Danny Byrd got his slot on the Voyager which disappeared several months before, yet the last thing Harry remembers is piloting one of Voyager's shuttles in the Delta Quadrant. His efforts to make sense of the situation make his superiors suspect that Harry is a Maquis spy. He discovers that he is an alternate timeline and finds allies in strange places as he tries to return to his own reality.
On Holodeck 2, Kes' second birthday party is interrupted by the news of a spatial distortion. As the crew scatters to their duty stations, they discover that something has affected the inside of the ship and the corridors seem to be shifting. It becomes impossible to reliably get anywhere my standard means. Captain Janeway makes physical contact with the anomaly and is rendered unconscious, leaving Chokotay in command as an implosion ring continues to crush the ship. After exhausting all other courses of action, the crew is left with the most unlikely option of all.
As Tom Paris admits he's falling in love with Kes, Neelix's jealousy starts to get the better of him. But with the ship's food reserves down to 30% of capacity, the feuding pair are dispatched to an inhospitable planet in hopes of procuring more food. But atmospheric storms disable their shuttle, causing them to crash-land on 'Planet Hell' and cutting them off from Voyager. Trying to survive, they come upon some hatching eggs and are faced with two additional dilemmas - helping the newborn to survive and dealing with its returning mother.
Although Voyager is about to enter Bothan space, the Doctor orders Janeway to relax with her holonovel to help her deal with the stress of command. But the stress is magnified when she begins to see items and characters from the holonovel outside the holodeck. Neelix reports that not much is known about the Botha except that they are extremely territorial and that many ships have disappeared without a trace in their space. When the Botha rendezvous with Voyager, they launch an unprovoked attack. As they maneuver to resist the attack, Voyager's crew are overcome by hallucinations which disable everyone on the ship except the Doctor and Kes, whose nascent telepathic powers enable her to resist the hallucinations. The fate of the crew hinges on their ability to find a way to repel the psychic attack.
While on a moon looking for polyferranide deposits to reseal the warp coils, Chakotay sees an ancient symbol. The last time he saw it was on a quest to Earth with his father, who explained it was a blessing to the land left by descendants of the ancient Rubber Tree People. Following a warp signature leads Voyager to a planet which seems to use the weather to prevent their approach. Chakotay goes alone to meet the planet's inhabitants and meets the people worshipped by his ancestors as the 'Sky Spirits'. Meanwhile, aboard the ship, Kes has noticed an appalling lack of compassion in the Doctor's personality. She suggests that if he were ever sick, he would develop more empathy for the sufferings of his patients. He accepts her challenge, but his confidence is shaken by his experience with a 29-hour Livodian flu.
The crew is hailed by Ocampa colonists on an alien space station who, at long last, lead them to the female mate of The Caretaker, a mysterious being who may have the ability to send the U.S.S. Voyager home. As Tuvok tutors Kes in honing her rapidly maturing mental abilities, it's concluded that her burgeoning powers have been extremely underestimated. Tanis, a male Ocampa colonist, agrees to introduce Captain Janeway and her crew to an entity they call Suspiria, the female mate of The Caretaker. As the Voyager crew builds great hope of returning home soon, Tanis implores Kes to stay with her Ocampa people on the alien space station.
Kazon intruders board the U.S.S. Voyager and steal a Transporter control module. That collateral enables their leader, Culluh, to persuade rival sects to join together to conquer the Federation ship. Surprisingly, the mastermind behind the Kazon's scheme is an advisor with Cardassian, Maquis, and Starfleet tactical experience -- none other than Seska, the despised traitor and former intimate of Chakotay. When Chakotay learns that Seska devised the Kazon plot, he secretly sets out alone -- against protocol -- to thwart her. The Kazon are one step ahead of him and he's quickly captured and brutally interrogated. With their First Officer in the hands of the enemy, the Voyager crew braces for a dramatic showdown, but Seska has one more trick up her sleeve.
In search of precious tellerium needed to power the ship, Janeway, Tuvok, Torres and Neelix transport to an Alsaurian city occupied by the hostile Mokra. Tipped off to the U.S.S. Voyager crew's presence, Mokra soldiers capture Tuvok and Torres. During the commotion, Janeway is secreted away by Caylem, a local eccentric who believes she is his long lost daughter. Neelix is not discovered and transports back to the ship with the necessary minerals and the bad news that the others have been discovered and taken prisoner. As Voyager searches for its arrested crew, Janeway goes undercover, forced to rely on her own devices and the help of her odd new protector, Caylem, to break into the prison and rescue Tuvok and Torres.
When the crew finds a deactivated humanoid robot floating in space, Chief B'Elanna Torres is able to repair this mysterious mechanical 'man'. When it comes to 'life' the sentient artificial lifeform, Automated Unit 3947, explains that its kind is near extinction and asks Torres to build a prototype for construction of more units. In accordance with Prime Directive, Torres must decline the request, but when 3947's Pralor homeship is located, the robot abducts her and threatens to destroy Voyager unless she constructs the prototype. Torres discovers that the robots are programmed to achieve victory while Janeway and her crew, taking measures to rescue her, find themselves in a war of alien robots.
After Voyager is severely attacked by Kazon and one of its crewmen killed, Chakotay appeals to Janeway to start thinking more like the Maquis. Janeway knows she must strengthen Voyager's position in the quadrant and, although it's a difficult decision and is against her beliefs and training, she agrees to take steps toward a strategic alliance with leaders of several Kazon factions. When they come together for a conference, its eminently clear that there are no rules in this region of space. Unbeknownst to Voyager, there is a traitor in their midst. Seeking an intermediary to begin talks with the Kazon, Neelix shuttles to Sobras, a planet with a Kazon settlement. There, he makes contact with an acquaintance -- Jal Tersa of Kazon-Pommar. Meanwhile Janeway's initial meeting with Culluh and Seska is unsuccessful but Neelix is able to befriend Mabus, a governor of the Trabe, an exiled sect and bitter enemies of the Kazon. Thinking that the Trabe have compatible goals of peaceful co-existence, Janeway forms an alliance with them -- with deadly results.
Lieutenant Paris makes history by becoming the first person to make a transwarp flight. But soon after his shuttle returns from warp ten he undergoes startling biochemistry changes. His cell membranes begin to degrade and despite the Doctor's best efforts, Paris dies. Hours after the pronouncement of death, Paris is discovered breathing, his body going through accelerated mutations which leave him radically transformed into a bizarre and terrifying cross between a human and amphibian.
When a crew member is murdered, Tuvok's investigation leads to another crewman, Ensign Suder, who finally admits he is the perpetrator. Vulcan instincts prohibit Tuvok from determining a logical motive for committing such a crime, so he attempts to understand the violent impulses of a criminal by performing a mind-meld on Suder. When Tuvok removes himself from duty, the Doctor initiates treatment which removes Tuvok's emotional suppression abilities. Meanwhile, Chakotay puts Paris on report for running an illegal gambling operation and Neelix embraces his role as the ship's Morale Officer.
Voyager spots a Cardassian designed, self-guided missile carrying a warhead capable of significant destructive force. As it travels toward Rakosan, a heavily populated planet, Torres reports that she's partly responsible for its virtually unstoppable status. When she was a Maquis, she intercepted the missile and changed its program to assault its own makers, but it later went astray and now she's the only hope I stopping it. So Torres volunteers to transport to the missile's interior and reprogram it again. But before she can detonate the warhead, the onboard computer tries to destroy her first, meanwhile Jonas transmits classified information on the mission to Seska.
A rebel Q escapes imprisonment from inside a comet and demands asylum aboard the U.S.S. Voyager. Just as quickly, the well known Q arrives to force the escaped Q back to the continuum, the extra-dimensional domain in which their immortal kind exist. Meanwhile, the escaped Q proclaims that if Captain Janeway grants him sanctuary, he intends to commit suicide to end the tedium he has endured as an immortal being. Noting the dictates of Starfleet protocol, Janeway holds a hearing to consider the request for asylum. The tables are turned on Q as a Federation personnel preside over a trial in which he must defend the Q Continuum and the ever logical Tuvok acts as counsel for the escaped Q. A courtroom drama ensues when Q calls himself to the witness stand along with a varied group of other people including Commander William T. Riker, whose lives were profoundly changed by Q's influence.
Voyager detects a distress call from a weakend lifeform aboard a small spacecraft and quickly beams a deathly ill Vidiian female to Sickbay. The doctor starts treating her for advanced stages of the phage by transferring her decaying body into stasis and creating a temporary, healthy holographic program of her being. As he becomes aquatinted with the alien, a hematologist named Danara Pel, something momentous occurs -- his adaptive program allows him to experience love and romance for the first time. Lieutenant Paris continues to be insubordinate and espionage is more complicated than Jonas thought when Seska instructs him to plan an accident which will damage Voyager's warp coils.
Neelix, a suddenly self-proclaimed journalist, hears a rumor that a fellow crew member has expressed displeasure with Starfleet and requested leave. Soon Tom Paris is relieved of duty to become a pilot with a Talaxian convoy -- leaving a saddened Voyager crew behind. Almost immediately, the Kazon-Nistim and the scheming Seska attack the Talaxian fleet, kidnap Paris and attempt to coerce classified information from him. Meanwhile Neelix suspects someone aboard Voyager has been secretly communicating with the Kazon and his sleuthing leads him directly to Paris.
Astounding consequences occur when the U.S.S. Voyager, while attempting to evade a pursuing Vidiian vessel, enters a plasma cloud. Before they can clear it, the engines stall, anti-matter supplies drain and a proton burst, originating from within the ship, cause heavy casualties and breaches the structural integrity of the hull. When Ensign Kim and Kes disappear into a void in space, Captain Janeway discovers that a duplicate Voyager with an identical crew exist in a parallel universe.
Tuvok and Bennet's shuttle crash lands on a sacred haven for the Drayan, an alien race which has shunned outside contact for decades. While Bennet lies dying from his injuries, three frightened Drayan children venture out from hiding. The young ones tell Tuvok that they have been abandoned by their people to die on the planet, and beg his help in saving them from the imminent arrival of the morrok' -- the messenger of death. While Tuvok tries to calm the tiny trio, he cannot comprehend why a society would forsake its own children. Then, during the night, two of the youngsters mysteriously disappear. Meanwhile, Janeway makes contact with the Drayan's First Prelate, Alicia, and in the course of trying to rescue Tuvok and the remaining child, there is an amazing revelation about this mysterious race.
The U.S.S. Voyager activates an automated message from members of the Kohl settlement, who, years earlier, survived an environmental catastrophe by submitting themselves into artificial hibernation. When the crew transports the Kohl's hibernation pods on board, they find humanoids in deep stasis with suppressed metabolic activity -- but with active minds and complex sensory systems controlled by a computer. In an effort to help the Kohl people, Torres and Kim equip two pods with Starfleet technology and submit themselves into stasis. With their mental and physical activities closely monitored, they enter the environment created by the computer attached to the Kohl pods. Once there, Torres and Kim find that the humanoid's dreadful fears about recovery and survival have caused their computer program to manifest a devious, omnipotent clown - the idealization of their fear - and a cast of other nightmarish characters. Then, the clown holds Torres and Kim hostage while making increasingly unreasonable demands of Janeway.
A Bizarre occurrence causes Neelix and Tuvok, who are attempting to transport back to the U.S.S. Voyager from an away mission, to arrive aboard the ship as one. The crew is astonished when a strange but oddly familiar alien humanoid with dark speckled skin and pointy ears - which is neither Tuvok nor Neelix - appears. The Doctor's bio-scanner shows that Neelix and Tuvok's patterns have merged, causing the pair to become one entity - Tuvix. While Tuvix assimilates and starts to become a valued member of the team, Kes struggles with the fact the Neelix may not be a part of her life anymore. Meanwhile, the Doctor devises a method to restore Tuvok and Neelix, except for one variable - Tuvix does not want to die. When the Doctor, who is programmed to follow certain ethical guidelines, cannot perform the separation, Janeway is left with a monumental decision.
When Janeway and Chakotay contract a deadly virus from an insect bite, the Doctor cannot find a cure. Unable to perform her duties, Janeway is forced to turn over permanent command of the ship to Tuvok and retreat, with Chakotay, to a small planet which shields the effects of the fatal disease. As the U.S.S. Voyager moves out of communication range, Captain Janeway leaves Tuvok with strict orders not to contact the Vidiians for help, even though they may have more sophisticated medical technology to handle the crisis. While the ship's crew is stuck with the harsh reality of abandoning their leader and first officer forever. The former Captain and Commander, alone on a strange planet, awkwardly drop protocol and begin to explore another side of their relationship.
In an emergency message to Chakotay, Seska discloses that their newborn son has been banished by Culluh to a servant colony. Chakotay feels conflicted about rescuing the baby because he was manipulated into fatherhood by Seska. When the crew detects a distress signal from a Kazon shuttle, they transport aboard the critically injured Teirna, a former aide to Seska, who delivers the news that Culluh has killed Seska. So, with Teirna restricted to secured quarters, the U.S.S. Voyager heads on a rescue mission through the Kazon-Nistrim territory where Kazon raiders viciously attack the ship.