The Andromeda picks up a group of refugees who have been subjected to psychological and physical torture.

Dylan finds himself on Seefra-1, one of nine identical planets orbiting two suns. He soon encounters Rhade, who has abandoned all hope. Rhade hates Dylan for the hope he has brought, and when someone asks Dylan be killed, Rhade agrees to do it.

Dylan runs into a problem while analysing a black hole and imagines what his life would be like with a family before the common wealth fell.

As the Andromeda responds to a distress call from a planet on the brink of destruction, the crew intercept a transmission from a ship returning to the surface. After seeing the message from Rev Bem the crew loads up to save him from the planet. As Rev is following the path of the Divine flashbacks occur of the Andromeda crew to help him on his way.

Dylan plays a dangerous game against two gamblers, but not everything is as real as it seems.

Dylan receives a mysterious package, but is then framed for the murder of its sender so Dylan and Harper go on a mission to clear his name.

After receiving a message from an unknown planet 3 days in Slipstream away, the crew of the Andromeda take it upon themselves to save the people. The strange thing is that the message is a woman and it is going directly into Dylans head and no-one else can hear it. As they enter the ice moon of one of the planets, they come upon the Vault of the Heavens. A large palace made of ice. in discovering this the comm is cut and on Dylan's orders, Try destroys an energy cloud above the planet. After discovering that the aliens mean no harm, Dylan finds out that they need the cloud, or the entire species will die! Will they be able to return the cloud before the time runs out?

After being repeatedly attacked by bounty hunters after several evasive slipstream jumps, Dylan determines that there must be a mole on board. After analyzing data recordings, he discovers that Beka has been infected by The Abyss and has unknowingly been giving away Andromeda's position. Dylan and the crew have to come up with a way to rid Beka of The Abyss -- without killing her.

The crew is tormented by a mysterious stranger who accuses them of murder.

After rescuing some people from a storm, a 'maggot' is brought onto Andromeda. This maggot chews through the systems and activations an old hologram of a crew member. This member had sealed himself in one of the hidden decks before the event horizon and had some through it. Believing that Dylan has betrayed the Commonwealth, an avatar and android of the crew man takes over the ship to bring Dylan to justice...

Dylan and Rhade receive a month-old distress signal from Beka. After following the coordinates she left, they find the Andromeda dead in space. On board, he finds Darregacorp engineers trying to salvage it, led by Jonah Derrega, and Beka Valentine.

When a valuable painting gets stolen after Beka, Rhade, and everyone else in the bar inhales a mysterious mist, Dylan jumps at the opportunity to win the reward for reclaiming it so the Andromeda can be repaired. After tracing the nanobots in the mist, they encounter Harper who is accompanied by a beautiful woman named Doyle. But Harper is caught up in the plans of Marika, who wants him to genetically engineer Vedrans, as well as to take over the Seefra system.

The unexpected return of Flavin takes Dylan on a journey through time, revealing mysteries surrounding Tarn Vedra, the Paradine, the battle with the Worldship, and Trance.

Dylan and Rhade attempt to infiltrate a mining camp where crystals are extracted, which contain the power needed to restore the Andromeda and leave the Seefra system.

The arrival of Trance's sun threatens to destroy all the planets except Seefra-1 unless the system problem is fixed.

The avatar of the black hole, that trapped Dylan after the Nietzschean ambush, returns to get him back.

The Andromeda is on the edge of a dimensional portal searching for Beka and Tyr, but when they return things may not be as they seem.

After finding out that a planet is developing nova bombs and testing them on nearby star and planet, Dylan takes it upon himself to disarm them. The commonwealth refuses to help so its a mission for the Andromeda and her crew!

A seemingly psychotic "Collector" simultaneously takes credit and blames Dylan for the fall of the Commonwealth. He also claims to be hosting (or holding captive?) the Triumvir Tri-Jema. The crew must decide whether to accompany Dylan on yet another odds-defying journey to save the Universe or to retire in relative safety.

When a slipstream event is detected in the Seefra system, Dylan, Rhade, and Beka try to find it, and their way out. Meanwhile, a man claiming to be from the future approaches Doyle, addressing her as Andromeda.

The evacuation of Seefra-5 is at risk when a religious sect decides to stay on the planet.

Dylan sets out to find an assassin known as The Leper who is trying to kill his good friend.

Tyr receives a communication from a human on an abandoned planet and leaves to meet her. As he does, a mad scientist boards the Andromeda using dark matter ninjas. After beating them, the man introduces himself. He loves the woman Tyr is with and wants to kill her, if he cant have her, nobody can. After saving her, he forgives her and lets her live. The episode ends with Tyr revealing that she is actually a Neitzian, the last female from Codiac, Tyrs pride. He says that he wants them to start a new Codiac pride but she refuses and Tyr leaves.

A power-hungry citizen seeks to manipulate the Commonwealth for his own gain. Dylan receives an unsettling view of his future from a prophetic alien.

The crew searches for a princess abducted by a ruthless pirate. As usual, nothing is as it seems. Along the way, a secret from Beka's past is revealed.