Dr. Rachel Finn née Riley
Xander Finn & Talia Rhade

Thousands of years in the future, the Systems Commonwealth is a republic based in a distant star system, Tarn-Vedra, and spans across multiple galaxies. The Commonwealth is at war with the Magog. Peace talks lead the Commonwealth to cede a key world to the Magog, one which belongs to the Nietzcheans; in response, the Nietzscheans secretly attempted to usurp control of the Commonwealth. Dylan Hunt is the captain of the Commonwealth ship, Andromeda Ascendant. Caught by surprise in the first engagement of the Nietzschean uprising, the crew evacuates on his orders with the exceptions of his future sister-in-law and CMO, Dr. Rachel Finn, and his chief helmsman, Refractions of Dawn. Dawn, however, is brutally murdered by Dylan's First Officer and best friend, Gaheris Rhade.

Like most other Nietzscheans, Gaheris had begun to resent the Systems Commonwealth for its decision to make peace with the Magog instead of destroying them outright. Anti-Commonwealth sentiments in the community reached a boiling point until they felt the Commonwealth's betrayal of them demanded retribution. Gaheris voluntarily sabotaged the Andromeda and engaged in a firefight with Dylan. He ultimately died in this fight, and the Andromeda was trapped in the mouth of a black hole, where it, Dylan and Rachel were frozen in time for nearly 300 years. When the ship is removed from the event horizon, the two find themselves engaged with smugglers trying to take over their ship to sell it to the highest bidder. After subduing and recruiting a few of the smugglers -- ace pilot Beka Valentine, brilliant but loony engineer Seamus Harper, mysterious medical officer Trance Gemini, pacifist Magog Rev Bem, and Nietzchean mercenary Tyr Anasazi -- Dylan and Rachel set out to restore order and peace to the known galaxies by resurrecting the Systems Commonwealth.

Rachel spends most of her days in conference with Dylan, advising him on the best courses of action alongside Andromeda's AI, while training Trance in proper medical care as she's apparently self-taught in-between patching up whatever wounds the crew manages to acquire. In private, however, she mourns the loss of her son and husband. Dylan understands her pain all too well as his fiancée, her sister, has been lost to him in their 300 year absence but while his heals to become a dull ache, Rachel's pain is constant and never-ending. Rev Bem and Rommie, Andromeda in android-form built by Harper, take notice of this and begin to counsel her. Together, they set out to solve the mystery of what happened to her family after her son's evacuation from Andromeda and the fall of the Commonwealth 300 years ago, hoping it will help her find peace. Initially, Rachel is enthused and welcomes the help with great hope until they discover that both her husband and son are dead. Her son, Xander, had apparently never survived his evacuation off Andromeda, his escape shuttle having been shot and destroyed by the Nietzcheans; Christopher, a Commonwealth navigator and slipstream pilot, had been listed among the dead at a battle just four years later. After a series of missions where she exhibits death-seeking behavior, Tyr orders her to shape up or he'll see to it that she's dropped off at the nearest backwater planet because they have a hell of a lot of work to do and her death would do no one any good.

"You are a brilliant doctor, Rachel Finn. Human, but brilliant. Despite the flaw of your race, I can appreciate that. Plenty of people still need you, girl. You cured Harper of Triangulum Measles, a disease that had been nearly extinct in your day but has ravaged planets unchecked for centuries. Imagine what else you could do. Imagine all those you could save. You can't do that if you're dead."

"I never pegged you for an idealist, Tyr. Or that you cared so much."

"Don't mistake my words for empathy. I care about the efficiency of this crew. Without you, we are less efficient and that puts everyone – most importantly, me – at risk."

"How very Nietzchean of you."

"As a doctor, you carry the weight of every living soul you take under your care. Take my advice: don't carry the weight of the dead, too. And if you wish to continue your fatalist behavior, you are more than welcome to channel that aggression into more productive means."

Rachel takes up Tyr on his offer and begins to train with him, taking all of her pain and anger out on him. As a Nietzchean, a species genetically engineered for perfection, he can handle everything she throws at him and is more than pleased when she becomes a worthy sparring partner. Her skills are put to the test when the Magog Worldship appears. A huge structure of twenty connected planets and an artificial sun, it contains trillions of Magog and is equipped with a powerful point singularity projector, which creates miniature black holes. Andromeda is heavily damaged in their encounter while Rachel, Tyr and Harper are abducted to the Worldship. The rest of the crew are badly injured and, trying to save his friends, Rev Bem puts himself at risk by entering the Worldship.

Dylan and Rommie venture onto the Worldship to rescue their missing crew and succeed, only Tyr and Harper have been infested with Magog eggs. Because of his superior genetics, Rachel is able to safely remove them from Tyr but Harper, a human with an already weakened immune system from growing up in a refugee camp on Earth, would've died in the attempt. Rachel vows to find a way to save Harper, who refuses to accept his eventual death when the baby Magog come clawing out of his body. With Trance and Andromeda's help, Rachel eventually manages to create a drug that'll temporarily halt the Magog gestation to buy them time until they find a way to safely remove them. As time begins to run out for him, Harper creates a Tesseract Machine with the help of a brilliant Perseid, Hohne, to remove the eggs. However, his device unintentionally begins to trigger ripples in time that cause parts of Andromeda to start shifting to other time periods, the past and the future. Rachel and Dylan find themselves back in the battle that started the Fall of the Commonwealth, that battle that left them stranded on the edge of a black hole and changed their entire world.

Rachel manages to find her six-year-old son Xander in the chaos and holds onto him, refusing to let him leave her arms lest he be swept back to the past when another ripple passes through. The entire crew manages to navigate the ripples and meet up with Harper in his machine shop. The eggs are hatching and he only has a few minutes left to live and they realize that they have to choose: if they activate the machine, they'll get the larvae out of Harper but Hohne will remain dead and a Trance from their future stays, or they can destroy the machine which would save Hohne and bring back their Trance, but Harper would die and, ultimately, so would Xander as he'd disappear back to his time. While the crew argues this, Rachel vehemently refusing to trade her son's life for Hohne's, the new Trance reaches out and turns the machine on, removing the larvae from Harper.

"I know I should regret what's happened, the things I said. As a command officer, I should've kept a level head and found a diplomatic solution but...as soon as I saw him, Dylan, I knew I couldn't let him go. No matter the cost. Not again."

"I understand, Rachel."

"No, you don't. You can't possibly understand. You're not a father, Dylan. He's my son. He's my son. And he's alive! I was given a second chance, to save him instead of sending him to his death. What other choice did I have?"

"Rachel, you didn't--!"

"I put him on that escape pod and the Nietzchean's blew it up. If I'd kept him with me, like he begged me to, he never would've died. I'm sorry if our relationship with the Perseid's is fractured as a result, but I am not sorry for choosing my son's life over Hohne's. I'm not and I never will. So don't ask me to be."

As time passes and the state of the crew changes. Tyr betrays his friends to become the leader of a unified Nietzchean force, separating them from the restored Commonwealth once again. Replacing him is Gaheris' identical descendant, Telemachus Rhade, a proud Nietzschean who doesn't accept his race's betrayal of the Commonwealth and agrees to help the crew. Despite having met Rhade on a previous occasion, Rachel struggles to distinguish him from his ancestor that essentially ruined her life. While her standoffish behavior doesn't bother Rhade, her fierce protectiveness and demands he stay away from her son do. As a father himself, the very idea that he would harm a child greatly offends him. As a means to bond with her, he offers himself as a new trainer to replace the lessons Tyr began. While Rachel is hesitant to accept, she accepts on Dylan's orders and finds it therapeutic to fight him and work through the lingering issues she has with his ancestor's betrayal. These sessions help form a deep friendship that, to both parties surprise, leads to love.

Using the coveted Route of Ages, a portal connecting all galaxies together, the crew defeat the Abyss that has been controlling the Magog and plaguing the galaxy. After killing Tyr, the Route closes before the Andromeda can escape so Dylan requests Trance's help. Trance reveals she is an Avatar of a sun, with the power to create and destroy, and so she destroys Andromeda and re-creates it in the correct universe. All seems well until it is discovered that the Magog Worldship has resurfaced and is headed for a pacifist planet, Arkology. Andromeda tries to defend Arkology but is horribly outnumbered and destroyed with all its inhabitants. Rhade, Beka and Rachel are left in absolutely hopeless situations, with Xander badly injured. Rommie explodes after being shot through her stomach while saving Harper from the Magog. Trance asks Dylan to escape on a slip fighter through the Route, claiming that now there is nothing more important than saving his life. Reluctantly, Dylan reluctantly leaves through the Route while Trance turns into a sun and crashes into the Worldship on the Andromeda.

The crew finds themselves transported into the Seefra system — nine identical barren worlds with a superstitious population and two dim suns — scattered in different locations and points in time. Technology (especially spaceflight) is shunned, and water is treasured because of constant drought. Harper believed himself to be stranded the longest; three years alone, trying and failing to rebuild Rommie, ultimately creating Doyle instead. The truth, however, is that Rachel had been stranded in the desolate system the longest: ten years. While trading in a marketplace on Seefra-4, Dylan and Rhade find themselves in a skirmish and arrested then bought and sold to a young man who informs them they are to be entertainment for the masses. Gladiatorial fighting was apparently popular for the people and, finding no escape, the pair are forced to fight to the death. Presiding over the fight is none other than Rachel, the last of Dylan's missing crew. The kind and compassionate doctor has become the ruthless leader of a small outpost. At least, that's what it appears to onlookers as, in private, she is still a loving and gentle mother to her two children. As Dylan and Rhade discover, the young man who'd bought them at the market was Xander, now eighteen, and he has a ten-year-old half Nietzchean sister, Talia. Rachel confesses that Talia is Rhade's, and that she discovered she was pregnant not long after she awoke on Seefra.

All of Dylan's crew are all angry with him for leaving them behind in the Battle of Arkology and for throwing them to Seefra without any way to get back to the Known Worlds. Their loyalty is strained several times, but is finally reaffirmed after the intervention by a Paradine sent by Dylan from an alternate future. Andromeda's power is eventually restored, but it is still unable to leave Seefra, which seems to be located in a "pocket universe," and the only way out is with the Route. Seefra turns out to be Tarn-Vedra, long lost capital of the Commonwealth, but the Vedrans themselves left it long ago, disillusioned with humans. Seefra-1 is the original Tarn-Vedra and Seefra-2 to 9 are copies of it. Tarn-Vedra's original sun was somehow replaced by two artificial constructs, Methus-1 and Methus-2, the former of which is now damaged and emits deadly flares, which are the reason for Seefra's drought. The Methus Diagram — a blueprint for Seefra system — also reveals the purpose of the eight extra planets: the Vedran sun will return someday, and destroy Seefra-2 through 9 to slow down and take its position. But, because of the damage to Methus-2, this mechanism is not working and the sun threatens to devastate the system completely.

After Andromeda is restored to full power, Trance's sun enters the Seefra system, and the people are safe on Seefra-1, the Andromeda slipstreams back to the Known Worlds where they discover that only four days have passed since the Battle of Arkology, and the Magog Worldship is crippled but still operational. Rhade reunites with Jillian, his first wife, alongside Rachel, Xander and Talia. While Rhade wishes for Rachel to stay with Jillian and their children, he knows that her place on the Andromeda. Her place is by his and Dylan's side in battle, although she agrees that Xander and Talia should stay behind. Xander reluctantly agrees but swears to protect their family until they return.

Andromeda visits Earth, where Harper secretly planned to stay, but as soon as the ship arrives in the system, the planet is promptly destroyed. A huge Nietzschean fleet emerges from behind the debris and Andromeda barely escapes. After a massive battle with the Nietzscheans, Dylan checks the Methus Diagram once again and discovers that Trance's sun is capable of destroying the Abyss once and for all. Andromeda returns to Seefra through the Route, followed by the Abyss. Trance manages to pull her sun closer and plunge it into the Abyss. With the Abyss finally destroyed, the battle is over. The Route transforms into a slipstream portal, allowing the Commonwealth fleet to return to Tarn-Vedra. While Beka, Harper, Trance, Doyle and Rommie stay aboard the Andromeda, Rachel retires her command in favor of taking up a civilian life on Tarazed with Rhade, who opts to return to his political position so they can be with their family.