Dylan Hunt is betrayed by his 1st officer when the Nietzschean prides betray the Systems Commonwealth. Stranded on the event horizon of a black hole, Dylan is frozen in time until a salvage crew try and claim the Andromeda.

Dylan must protect the Andromeda from the mercenary crew after sleeping the "long night", while Beka and her friends discover they may be fighting for the wrong person.

Dylan is manipulated into unlocking powerful weapons stores when the Andromeda discovers a Commonwealth space station populated by children who believe that he is the legendary' High Guard' who has come to bring peace by destroying their enemies.

Dylan and the crew of the Andromeda face off against an unknown enemy when they discover a ship's recorder, forcing Dylan to deal with the tensions between him and his new crew.

The Andromeda finds a Nietzschean colony conducting pirate raids on a nearby Than planet. Dylan hopes that saving the Than will win support for his cause, but Tyr's loyalties are divided when the colony presents him with the opportunity to have a mate and a home if he gives them the Andromeda.

When a slipstream error throws the Andromeda back to the climatic battle of Nietzschean-Commonwealth war, Dylan and his crew must not only decide whether or not to interfere, but which side to interfere on. Ultimately, its discovered that the Nietzscheans arrived with 1,500 ships, three times more than was said to have been in the battle and they realize that their intervention is necessary to preserve history. With no choice, Andromeda attacks the fleet and wipes out most of it, with Tyr revealing he knew the truth about the fleet size all along from a Nietzschean legend, but their history had no idea that it was the Andromeda that was responsible. With history back on track, Andromeda returns to her own time.

Beka's brother and his friend come aboard, with her brother claiming to have converted to Wayism. However, it soon becomes clear that they have an agenda of their own, connected to the 'Resters', a group of environmentalists attempting to prevent all space travel.

Dylan is able to communicate with his lost love via a black hole as the Andromeda faces off against Nietzscheans, but when faced with the chance to be reunited with her by transporting through time, he must choose whether or not to return to the past and abandon his new mission. The rescue fails when the ship comes under attack, with the attack damaging the ability to rescue Andromeda. Dylan, who had teleported aboard, takes command and has the crew push Andromeda as far out of the black hole as it can while he contacts the Nietzscheans and demand they leave or face Andromeda in battle. The ruse works and the Nietzscheans leave. Dylan says goodbye and returns to his own time where he learns that while the efforts in the past failed to save him, it made it possible for the Eureka Maru to save him in the present, so the effort was not in vain. Guest stars Sam Jenkins, Kevin Sorbo's real life wife, as Sara Riley, his lost love.

Dylan and Andromeda are imprisoned on a penal colony where no-one is allowed out; even the inmates' children are forced to remain. As the ship's avatar's power source runs low, Dylan looks to an intelligent woman to help them escape. Meanwhile, with the help of Trance, the crew tracks down Dylan and Rommie's location and try to reach them in the Eureka Maru, but face the colony's defenses which threaten to destroy the ship. Dylan stages an uprising against the android warden of the prison and tries to shut down the defenses so that the Maru can rescue him, but is no match for the warden who kills the person helping him. Rommie, knowing Dylan is in trouble, is able to use an improvised power source to give her some power and intervenes. Rommie destroys the warden, but runs out of power before she can do anything else. Dylan manages to shut down the defenses in time and the Maru safely lands and rescues him and Rommie, but Dylan is left perplexed at how Trance randomly picked the right prison planet.

Castalians come aboard to finalize the charter of the New Commonwealth, but, when their leader dies, Tyr becomes the prime suspect due to the leader having destroyed a Nietzschean ship during an old war.

Beka and Trance search for Beka's father's former business partner and discover he is the leader of a large company dealing in a highly addictive drug; meanwhile, the rest of the crew organise a 'garage sale' to gather money for new parts.

The Andromeda discovers her sister ship, the Pax Magellanic, with a skeleton crew who have not aged a day, only for Andromeda to struggle with the ship's demented AI as the crew try to piece together the mystery of what happened to the ship to remove its slipstream drive and render the crew immortal. Its eventually revealed that the crew are all android versions of themselves except for the First Officer who is in fact the ship's Avatar like Rommie is to Andromeda. Its revealed that the ship ejected its Slipspace drive to destroy a nearby planet. The ship attacks Andromeda, but Dylan orders fire only directed at its weapons in order to disable it. To everyone's surprise, this results in the ship's destruction and the AI, in a final transmission reveals why: only wanting death, it lowered its defenses so it would be destroyed to the sorrow of Andromeda.

With the Eureka Maru having been infected by attack-nanobots that disrupt electrical systems, Tyr crashlands on a Nietzschean controlled planet, his memories lost and the Maru damaged, and must try and remember his past before the ruling Nietzschean pride discover him and the crate he was transporting.

Harper becomes a genius when a Perseid "downloads" immense amounts of knowledge into his brain, and becomes the target of a bounty hunter with advanced technology. Dylan and his crew discover information on the Magog.

While picking up parts for Andromeda, Dylan Hunt is arrested on charges for assassinating a planetary dictator three hundred years ago, by one of the men who participated in the assassination, leaving Trance to rescue him and solve the mystery of how the man survived for three centuries. Its eventually revealed that the dictator was killed in self-defense by Gharis Rhade, but the man set to replace him became as bad as he was and survived through cloning. When Dylan and Trance confront the man, Trance offers a peaceful solution, to abdicate power to the government and include the rebels in the new government that forms so that everyone has a voice. The man, who never wanted to become what he did, agrees.

The crew is contacted by a drone from the Consensus of Parts, a race of sentient machines who live in the space between galaxies, who has been sent to make contact with them, but face danger when the drone takes over Andromeda in an attempt to escape his destruction while his 'master' tries to force Rommie to join the Consensus.

Gerentex kidnaps Trance and Harper and forces them to assist in his quest for power, as he claims to have discovered the location of a map to the lost Commonwealth capital Tarn-Vedra.

While the rest of the crew of the Andromeda aid in relief efforts for a Than colony, Dylan and Rev Bem go to the aid of one of Rev Bem's friends to help protect a peaceful people against slavers, but matters become complicated when it is revealed they possess a perfect genetic memory, if Dylan teaches them to kill, their descendents will always remember how to take a life.

Dylan tries to bring peace to two warring Nietzschean prides by escorting a princess of one to an arranged marriage with the other, but when Dylan and the princess are forced to escape in the Eureka Maru while Andromeda lures away a fleet, he realises that things aren't as they seem.

Rommie falls in love with an android who was rescued from a destroyed ship, but she is betrayed when it is revealed that he is the avatar of the warship the Balance of Judgement, who has gone insane after the Fall. The ship is the leader and founder of the Restor faction. Gabriel, who is controlled by his programing, infects Rommie with a virus so she broadcasts the crew's plans to the Balance, but the crew use this to draw the ship into a trap, destroying it by luring it in with an abandoned (except Gabriel and Rommie) Andromeda and then deploying missiles with proximity fuses from the Eureka Maru. Gabriel is set free, but Rommie is forced to destroy him after discovering that the Balance transferred a copy of its AI to him.

Beka attempts to pilot the Andromeda to Tarn-Vedra, a planet that is cut off from the slipstream. In a weakened state, she takes the drug Flash and overdoses, nearly dying.

Harper accidentally activates a hidden personality stored away in Andromeda '​s system, causing her to forget the events of the past few years and re-enact a top secret mission. While executing this mission, Andromeda becomes overrun by Magog.

With the ship severely damaged and Tyr, Harper and Rev having been abducted, Dylan leads the crew of the Andromeda in battle against its deadliest enemy to rescue their captured crew-members. With help from Rev who pretended to join the Magog, the group escapes and Andromeda launches a nova-bomb into the Worldship. However, due to the actions of the Spirit of the Abyss, the Magog leader and creator, the Worldship survives though severely damaged while Andromeda gets away, also badly damaged. The World Ship is discovered to be heading to the Known Worlds and now the Commonwealth, once a dream, is a necessity to combat this threat.

While Harper and Rommie try to cope with their recent 'violations' by the Magog. Dylan, Beka, Rev, and Tyr, pursued by a gang of Nietzscheans, are forced to make a crash landing on an icy planet, and must escape before Rev Bem's desire to feed either forces him to kill or causes his body to digest itself.

The crew must steal a jewel being fought over by a greedy Drift-owner and the Than to organize a peace treaty, but matters become complicated when Beka develops a relationship with the security chief on the station, who is a former thief known as 'Schrödinger's cat'.

While Andromeda investigates mysterious attacks on an isolated, somewhat xenophobic Inari, Trance is interrogated by that same species as they try to determine her origins, blaming one of her kind for inciting a recent war.

Dylan and crew attempt to find a long-lost Commonwealth leader and bring her back into the fold, but the question of her identity proves more complicated than it initially appears.

While Rommie tries to save a defector from a planet that hates AI's, the Eureka Maru plunges deep into the ocean after being crippled, leaving Harper, Tyr and Rev struggling for survival as Dylan, Beka and Trance attempt to stop a planet-destroying ship armed with Magog weapons.

With a deadly plague on the loose, Andromeda, captained by the inexperienced Harper while Beka seeks stragglers from the convoy, escorts medical ships through Drago-Kazov space while Dylan and Tyr try to stop the missile batteries trained on them.

Andromeda discovers a planet of Commonwealth survivors and descendants gathered together by Dylan's former fiancé after the Commonwealth fell, including the genetic reincarnation of Dylan's first officer Rhade, but when the election to rejoin the Commonwealth goes against Andromeda '​s crew, an apparent Magog attack raises several questions.

Another agent of the Abyss tries to tempt Harper to join the Magog god by removing some of his larvae, as the crew battles more tesseracting villains.

Dylan and Tyr are appointed the aides to a Prince after the rest of his family is killed in a civil uprising on his planet, but they find themselves facing significant challenges from the revolting nobles while trying to reinstate his rule and negotiate a peaceful settlement.

Dylan and his makeshift Commonwealth fleet, consisting of the Sabra-Jaguar pride, engage the Drago-Kazov fleet while Harper and Rommie return to Earth to start an insurrection, but matters are complicated when Dylan finds the fleet to be larger than he expected.

After Rev Bem departs to try to find himself, Harper, running out of time before the Magog hatch, must build a Teseract Machine to remove them with Houne's help, unintentionally triggering 'ripples' from the future that cause parts of Andromeda to start shifting to other time periods and culminate in Trance being replaced by her future self.

Dylan outruns dangerous mercenaries by kidnapping a Tourist barge and her pilot, while Tyr and Rommie must put aside their differences to find Dylan before the mercenaries do, leaving Harper to try to adapt to the "new" Trance.

When Dylan, Beka and Harper are called to identify the body of Beka's lost crewmate Bobby Jensen, they discover that he is actually alive and seeks to force the Andromeda to help end a revolution that he started after he left the Maru.

The Andromeda is pursued by the Than after they rescue dying people from a drift, but when the victims come back as the walking dead, it is revealed that they are under the control of a hive-mind-entity known as the Bokur that infects and kills its victims. With Beka infected and Trance being used as a vessel to communicate, Dylan, Rommie and Harper must race against time to discover a defence and save their friends before they are all infected.

Dylan, Beka, and Trance attempt to attain the mystic 'Engine of Creation', capable of rewriting the universe according to the designs of whoever possesses it, before someone else gets it, resulting in a brief encounter between Trance and another of her species.

During an investigation of a black hole, Dylan is blown out into space and finds himself married with a son in a world where there are no Magog and the Commonwealth is still intact (albeit falling from prolonged war). Episode is a clip show.

Dylan, Trance and Rommie must rush to save a Vedran, the long-lost founders of the Commonwealth, from the deadly Caldarens, but her demands after her rescue place Dylan in a difficult position.

A mythical planet-eating space creature turns out to be fact when it attempts to eat the Andromeda, with only Dylan and Trance in the Eureka Maru available to save the day as Rommie begins to shut down and the ship begins to dissolve.

While Dylan embarks on a quest to liberate captured ships of the High Guard from imprisonment with the help of their AI's, hampered by their unwillingness to become the slaves that they feel they would become if they gained captains once more, Beka is forced to convince the potential fiftieth planet in the New Systems Commonwealth to sign the charter without Dylan to win them over.

When Tyr races to save his wife and her colony from attack by the Genites, humans opposed to genetically-engineered humans (a particular problem as that includes almost all of the crew of Andromeda), he discovers that not only is he a father, but that his son may be the foretold genetic reincarnation of Drago Mussevni.

Mysterious beings begin attacking delegates at the final Commonwealth Charter signing that will determine the First Triumvant, but when Trance reveals that this crisis resulted in the destruction of Dylan's dream of a renewed Commonwealth, the crew must find a way to win a fight that they lost against in Trance's future.

When Beka and Tyr are taken over by the energy from a dimensional tunnel, they attempt to force Andromeda into the tunnel, leaving Dylan, Trance and Harper to stop them before the ship is destroyed.

After Dylan receives a strange map in the mail, he is framed for the murder of the contract killer who sent him the package, leaving him and Harper in a race against time to clear their names before Commonwealth Security catches them, as well as to find the pieces of a mythical vase said to grant the owner the 'blessings of the cosmos'... a piece of which Dylan acquired before his trip to the black hole.

After rescuing a group of refugees fleeing an oppressive dictatorship, the Andromeda crew face serious problems when the refugees are revealed to be severely mentally unbalanced due to government experiments, each of them brainwashed to believe that they're the doctor responsible for the condition of the others.

Andromeda transports Beka's Uncle Sid when he runs for the top government office in the newly reformed Commonwealth, but matters are complicated when a seemingly failed assassination attempt puts him in a coma and his company opens up a revenge account that sends bounty hunters after everybody likely to have put out the hit in the first place.

After an attack by pirates, Dylan, Tyr, Harper and Rommie encounter a spacecraft from Earth that set out to explore deep space hundreds of years ago, but tensions between the ship's captain and crew result in the Andromeda crew getting caught up in a mutiny as they try to repair the slipstream drive on the Eureka Maru

The Andromeda crew must stop the evil rulers of the planet Marduk from making weapons of mass destruction.

Dylan goes on a mission to seek out "The Leper" in order to prevent Marshall Man Ka-Lupe's assassination.

The Andromeda is haunted by a crew member who died over 300 years ago.

Tyr encounters a long lost love and the man who had hired him to kill her.

In an alternate universe where Dylan died before being trapped in the black hole, Gaheris Rhade sets out to restore the Commonwealth, but his increasingly strained relationship with his crew, to say nothing of his negative views on the Nietzschean prides, make this a seemingly impossible task. Episode is a clip show.

The mysterious race that attacked the first Commonwealth Charter signing returns, and it's up to the Andromeda crew to stop them again.

Trance runs through a series of possible outcomes in order to save the crew from a deadly intruder.

Dylan, Tyr and Beka fight to rescue the crew of a new, "More powerful than Andromeda", Commonwealth ship when it explodes, forcing the crew to suspect sabotage.

Beka puts her feelings for a past love ahead of the safety of her crew and endangers an entire planet.

The crew receives a cry for help from the long lost Rev Bem. Episode is a clip show

The crew battles against the Pyrians in order to save the planet Samsarra and avoid a galactic war.

Dylan is beckoned to a far off planet by the voice of a mysterious woman.

Dylan and the crew search for a Nietzschean slip-scout probe that enables one to map every meter of the slipstream.

Dylan and the crew take a wrong turn, ending up in the Prolon System, where they discover a princess who is not what she appears to be.

Andromeda and her crew set out to find a colony of Nietzscheans that have disappeared. Unknown to them, they aren't the only ones looking.

The Balance of Judgment returns, taking over a new High Guard ship and Rommie. Its revealed that when it was destroyed, it transferred a copy of itself into Rommie as well as Gabriel. Using Rommie, the AI takes over the Resolution of Hector and forces Harper to build it a new Avatar it names Remiel. Andormeda tracks down the ship and disables it while Dylan and Hector, the Avatar of the Resolution board the ship to stop Remiel and the AI. They free Rommie, but are unable to defeat Remiel who kills Hector. However, Rommie manages to break through to the Balance AI and convince it to stop, reminding it of its original purpose as a High Guard ship. Remiel refuses to give up and tries to escape, but Rommie and Dylan blow him into space. Later all traces of the Balance AI are removed from the Resolution and Rommie.

The Drago-Kazov clan begin a war against the Commonwealth and others. Tyr shows his true intentions. The Commonwealth fleet is lured into an ambush and destroyed.

Dylan receives a message from a collector claiming to have a hostage, and finds the remains of the Commonwealth fleet, leading them to the All Forces nullification point.

Citizen 8 threatens to replace members of the Commonwealth, including Dylan, with help from his foreseeing slave.

Andromeda encounters the builder of the Worldship and has to stop him before he launches another invasion by the Abyss. Ultimately the new World Ship is destroyed, but the bad guy manages to escape.

Dylan is kidnapped and forced to play mind games for the amusement and monetary gain of weapon dealers.

"File D", a flexy that can erase people's minds, is in the hands of two warring siblings, with Andromeda and Harper trying to prevent its activation.

Tyr Anasazi joins with the Collectors to find the Route of Ages, thinking it will stop the Abyss. Rhade, who lost Tyr as his prisoner, joins the Andromeda crew.

Beka and Tyr are pulled through the Route of Ages, where the crew of the Andromeda pursue and confront Tyr as he prepares to offer Dylan to the Abyss in exchange for Nietzschean safety in the upcoming war. Dylan and Rhade rescue Beka, but are forced to kill Tyr as they escape. After Andromeda gets trapped in the Route of Ages, Trance reveals her true nature as the Avatar of a Sun and saves the crew, though only Dylan is aware of the truth.

Fate brings Dylan full circle to fulfill a planet’s destiny three hundred years in the making when the crew return to a planet where a woman is supposed to merge with a power source. Dylan helps her do so and defeats the person trying to use her for her own gain and reveals that he was the mysterious soldier that had saved her life three hundred years before and never returned despite his promise because he got trapped in the black hole.

The crew thwarts an assassin’s attempt to steal the minds of the Commonwealth’s most brilliant scientists.

Dylan hunts down a notorious outlaw who has kidnapped a Commonwealth leader’s daughter. Things are revealed to not be what they seem: the daughter was set up to be murdered by her insane father and the outlaw is actually more of a Robin Hood type character rather than a villain. After stopping the woman's attempted assassination by her own father, Dylan invites the outlaw and his coalition of more than 1,100 planets to join the Commonwealth in exchange for his freedom and allowing him to marry the woman.

Dylan is arrested and tried by the Collectors and Triumvirs for high crimes against the Commonwealth.

When the Andromeda intercepts a shipment of Living Armor, Dylan goes in search of its creator and learns a deadly secret.

While trying to escape pursuing ships and low on fuel, Andromeda ends up in a dead galaxy and try to use a new device of Harper's, which accidentally transfers Dylan to an alternate universe where he died a hero after stopping the Nietzchean rebellion three hundred years ago and Andromeda has been turned into a museum. In the new reality, the Commonwealth never fell, but Harper, now part cybernetic and manipulated by the Abyss, has taken it over with Rhade as his second in command and Beka the general of the rebellion. Dylan teams up with the alternate Rommie and a part of Trance that enters that reality looking for him to stop Harper. With the help of Beka, Dylan leads a counter-rebellion on board Andromeda and tries to reach out to Harper, believing he still has good in him. Alternate Rommie and Beka defeat Harper's forces, but Rhade activates Andromeda's self-destruct. Harper, who Dylan did reach, decides to surrender, but Rhade kills him as the self-destruct reaches zero. However, Andromeda reveals she tricked him and orders Rhade to surrender as Harper's rule has now been overthrown. Beka and Rommie plan to work together to restore the Commonwealth to its former glory with the help of the Andromeda and Dylan has Trance return him to his world with Harper's device. Before she does, Trance gives him a "gift," the word "Almathea" and upon his return, Dylan finds out he has only been gone thirty seconds. There, he learns that by rigging up the Eureka Maru to the Andromeda, the ship can now reach a nearby star, but unless one goes supernova, they won't be able to refuel. Dylan learns that one of the stars is Almathea and orders Andromeda to it. Almathea goes supernova and Andromeda is able to refuel. Trance mourns the loss of Almathea as the star sacrificed itself for Andromeda.

The crew steps in to mediate an apocalyptic war in order to halt genocide and cure a fatal disease.

The Collectors trap Dylan in a life or death test using former crew member Rev Bem as bait.

The crew discover that Beka's behavior is being influenced by the Abyss after a Restorian attack, forcing Dylan to carry out a dangerous plan to rid her of its influence by travelling into Beka's mind. Dylan ultimately manages to trap the Abyss in a VR matrix, but it starts to take over Andromeda so Trance enters the matrix and uses her powers to defeat it.

Harper is captured by the Patriarch to build a bridge across time so he can bring an army of the future to the present, but the future is not what it seems.

The Triumvirate sends a beautiful spy to tempt Dylan and retrieve the Star Map.

Rommie’s emotional decisions sever her connections with the ship’s systems, leaving the Andromeda vulnerable to a Magog attack.

The Abyss sends agents to murder the True Collectors and find their hidden library.

ndromeda saves a transport from Arkology, a peaceful society on a space station, who is now the target of the Worldship. Dylan also learns of his true heritage as a Paradine. To be continued...

When Dylan can't move the Arkology, he chooses a stand off which he can't win. Things go badly: Rhade is surrounded, Rommie is destroyed, Harper is found by a Magog and Beka is presumably killed while Arkology is destroyed and Andromeda is invaded by Magog and severely damaged with the only survivors being Trance and Dylan. Dylan tries to destroy the World Ship by firing every Nova Bomb Andromeda has at it, but does little damage. Andromeda repels the Magog by venting her atmosphere and Trance convinces Dylan to abandon ship in a Slipfighter for the Route of Ages while she deals with the World Ship. As Dylan heads into the Route of Ages, Trance pilots Andromeda into the center of the World Ship, firing every missile the ship has as she goes to clear the way, saying her goodbyes. As Andromeda loses power, the ship enters the center of the World Ship and Trance goes supernova apparently destroying the World Ship. Dylan enters the Route of Ages where he encounters another version of himself. The two Dylan's stare at each other for a moment before the other one walks away.

Upon discovering the truth about planet Seefra-1, Dylan must free its people and reunite his crew. In the end, Dylan reunites with Rhade and sets out to find the others, having learned that Seefra-1 is actually Tarn Vedra, his long missing homeworld. To be continued...

Dylan and Rhade pick up a distress signal from Beka, only to find her scheming with a trade mogul who has claimed Andromeda for himself. The mogul tries to destroy Andromeda in the end, but Rhade sabotages his ship and Dylan realizes that the Core Creature is actually Trance in her sun form. Trance restores enough power to Andromeda for the ship to fire a counter-missile, but Beka is unhappy with Dylan leaving her in Seefra for what seemed like years and holds little loyalty to him anymore. Also, Trance regains her usual form, but seems younger than when she went supernova at Arkology, but not as young as when they first met her. However, she only holds a vague recollection of the crew and doesn't remember anything.

The crew reunites with Harper and the mysterious 'Doyle' when they confront a geneticist bent on an idea of a Vedran re-birth. In order to eliminate the tech ban that prevents her from realizing her goal, she plots to use fear to control the Seefra system.

For all of her life, Doyle has been plagued by amnesia and nightmares. When Argent, a "revolutionary" android from the future, arrives, Doyle discovers the truth about her life. Its discovered that Doyle is actually an android herself, created by Harper to hold Rommie's core programing when he was unable to rebuild her. Argent tries to entice Doyle to join him, but Doyle refuses and Harper destroys him and his men as well as their tesseract, but in doing so also destroys a possible way out of Seefra for the Andromeda crew.

Beka is offered a mysterious prize by Virgil Vox, Seefra's only DJ, and must confront the tech police leader, Ard Barton, who wants it for himself. With the guidance of Virgil Vox, Beka learns the truth about the Seefra System and locates the mysterious Meethus Diagram, but is left with no clue as to its purpose.

Dylan and the crew encounter an officer of the original Commonwealth, who is trapped in a time loop. Its revealed that she was one of the scientists who pulled Tarn Vedra into the Seefra System and she helps correct the mistake that causes Seefra to be a desert. When the time loop is broken, she leaves and its unclear what happens to her, but on Seefra it finally rains.

Flavin returns to teach Dylan about his abilities as a Paradine, and a gang war over his ship and its technology ensues.

Harper discovers a crystal that can restore Andromeda to full power. In order to obtain some of the crystal, however, Dylan must become muscle for Cutter, the mine's owner, who uses slaves to extract it. The crew get the crystal they need, but are forced to use it as a bomb to destroy the mines as they free the slaves.

The crew encounters Orlind, a man who maintains a series of tunnels on Seefra-1, who leads them to a Vedran chamber containing portals that can be used to tesseract to the other eight Seefra planets.

After an old man named Prysis is slain, a mysterious man arrives through the Route of Ages to find his killer. Beka, Rhade, and Harper are the main suspects, and Dylan strikes a deal: the stranger will return Andromeda and its crew to the known worlds, in exchange for Dylan executing Prysis' murderer. In the end Dylan is killed, but its revealed that the stranger and Prysis are the same person after Dylan revives. Dylan realizes that the Stranger is a Paradine sent from the future to bring the crew back together as they used to be and he leaves behind a cube that has the potential to repower Andromeda.

The crew helps rebels on Seefra-5 who are battling a local warlord. In order to help them escape, Harper attempts to rebuild the quantum teleporter with assistance from another scientist thought to have been dead for years. This ultimately causes power to go out all across the planets and is restored when the scientist sacrifices himself to shut down the teleporter. The lack of power allows the rebels, led by Rhade, to defeat the warlord who flees the planet, but after he targets Andromeda, Dylan destroys his ship. Harper mourns his friend's death and discovers a message from him.

Beka's new boyfriend, Peter, places the entire crew in danger with a series of tests, culminating in a startling discovery that may help the crew – if they can escape the Seefra system. Peter is defeated by Dylan while Andromeda, now restored to full power, saves Beka. Peter leaves through the Route of Ages and Dylan reveals the startling truth: Peter was Drago Musevini, the progenitor of the Nietzschean race. He used Beka's DNA to create the Nietzscheans which makes her their Alpha Matriarch. If the Andromeda ever returns to the Known Worlds, this will give them an advantage over the Nietzscheans.

Searching for answers, Trance encounters a man claiming to be a sun god. Meanwhile, searching for treasure, Beka and Rhade become trapped together and must face a test that will either bestow wealth on them – or drive them to insanity. The man turns out to be the Avatar of Tarn Vedra's moon and his and Trance's meeting causes Trance's sun, the original Vedran sun, to return to the Seefra System. Trance and the man, Ione, rescue Beka and Rhade, but he and Trance can never be together so he tesseracts away.

Trance falls ill when she attempts to stall her sun, which threatens to destroy the outer eight Seefra planets and kill millions.

Harper builds a giant parabolic reflector in an attempt to slow down the Tarn-Vedran sun and delay its collision with Seefra's planets, while a mysterious entity threatens Andromeda and its crew. Its revealed that the entity is the Avatar of the black hole Andromeda had been stuck in for three hundred years and that she and Dylan had a relationship while he was stuck which he doesn't remember. Ultimately Dylan is forced to trap her in a data file while Harper's reflector fails to work.

As Trance's sun approaches, the crew journeys inside the artificial Methus-2 sun to repair it and fix the braking system that is supposed to guide Trance's sun into position. They also go in for more fuel for Andromeda. The crew succeeds in fixing the sun and getting the fuel, but Trance is replaced by a doppelganger.

After a lab explosion, Dylan finds himself travelling through a series of alternate realities.

Rommie turns on the crew after she is rebuilt to help evacuate Seefra's planets.

The crew's efforts to save the population of Seefra-5 are stymied when the warlord who controls most of the planet convinces his fanatical followers that the approaching sun is a technological deception designed to drive away the planet's inhabitants and leave the planet open to be looted.

The crew struggles to rescue Trance from Methus-2 and Harper from General Burma, Seefra-5's warlord, who the crew discovers is in league with the Abyss. Dylan and Rhade succeed in rescuing Trance who defeats her evil counterpart and drives her away while Dylan and Beka manage to kill Burma.

Trance's 'family' of sun avatars decides to destroy the Abyss – by expanding the All Forces Nullification Point until it consumes the Abyss and the three galaxies that make up the known worlds. Dylan also receives a message from Flavin who reveals that all of the Paradines have been killed and Dylan is the only one left. With the help of the leader of Trance's family, Maura, Andromeda finally returns to the Known Worlds only to discover that its only been four days since they left. They also learn that the Nietzscheans are planning an attack on Tarazed and the World Ship wasn't destroyed at Arkology as believed, just badly crippled. Andromeda heads to Earth where Harper secretly plans to stay, but the planet is destroyed by the Nietzscheans guided by the Abyss. To be continued...

The final battle to save the New Systems Commonwealth begins as the Nietzscheans destroy Earth and attack Tarazed. Rhade chooses to stay on Tarazed with his family while the rest of the crew choose to remain behind on Andromeda to fight despite Maura offering them a chance to return to Seefra through the Route of Ages which the Avatars have no intention of destroying. Andromeda manages to hold its own, but is no match for the fleet. Maura confronts Dylan and attacks him, revealing herself to be an Avatar of the Abyss and the one that murdered the Paradines. Trance intervenes and orders Dylan to take the ship through the Route of Ages to Seefra. Dylan complies and the Abyss destroys Maura for failing it. At Seefra, Dylan realizes that the Meethus Diagram is designed to show how to destroy the Abyss: burn it with Trance's sun. However, another Trance tesseracts in and demands they kill the first Trance, revealing that one of them is an imposter. After a brief hesitation, Dylan shoots the first Trance as the second Trance was crying and the Abyss has no emotions. The first Trance reveals herself to be the mysterious Virgil Vox and taunts the crew before Dylan kills her. The crew pilot Andromeda into the Route of Ages with Trance's sun being pulled along by her. The Abyss starts to emerge from the portal as they approach, but Andromeda is able to fly through it, pulling the sun in with it. Andromeda makes it out safely while the Abyss is destroyed. As the crew celebrate, the Route of Ages turns into a Slipstream portal, reuniting Tarn Vedra with the Known Worlds. A Commonwealth fleet arrives, Rhade among them, and Rhade reveals that the battle is over and his family is fine. As the rest of the crew leave to their tasks, Dylan celebrates the victory and the fact that after so long, he is home.