Resuming from the previous season, the Andromeda is on the edge of a dimensional portal searching for Beka and Tyr. In an attempt to save them, Harper has constructed a device to reopen the portal. Using this Dylan enters the portal in the Maru. As he returns to Andromeda without his missing crew members, they appear on the ship. With no explanation to where they have been, they both attempt to get the ship away from the dimensional rift. Beka and Tyr seem to be acting very strangely and Harper discovers that there is a signal coming from the portal that is controlling Beka and Tyr. As Beka tries to get the Andromeda to enter the portal and kidnaps Trance, Tyr kidnaps Rommie and then erases the ships core AI. Trance frees herself from Beka's restrains and fights her on the deck of the Maru.Tyr and Dylan then get into a fight while the Andromeda is slowly moving towards the rift. Harper manages to close the rift just as Tyr is about to kill Dylan. This severs the connections and Tyr and

Dylan is framed for murder in order to blackmail him for a shard he possesses.

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

Beka's Uncle Sid returns, as a candidate for a leader of the Commonwealth. He plans to use the Andromeda to help his chances, but an assassin has other plans for him.

As Dylan, Rommie, Tyr and Harper flee from the Ogami, they encounter a ship sent from Earth to explore space over 3000 years ago. As the ship is a giant engine, it travels so fast that the crew never age. As the Maru has no slipstream engine, Dylan is faced with a decision that could change the future of the commonwealth. Can the Andromeda come to the rescue?

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!

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

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...

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.

Gaheris Rhade sets out to reshape the universe according to his will and restore order amid the chaos

The Andromeda tries to stop mysterious attacks occurring on nearby planets and outposts.

The episode opens with Beka, dead on the floor of Command. She has a hole in her chest. Harper's body is propped against a machine, being electrocuted. Tyr lies on the floor of a deck, also dead. Dylan is leaning against some bars, bleeding. In Slipstream Control, Rommie is picked up by a large stranger in black armor, and thrown down to the Core. The stranger activates an overload, and the Andromeda splits in two, then explodes. Trance, in a mysterious blue space, watches in horror. She is with one of her Bonzai trees. ""Okay, that did not work."" she says, ""Let's try again.""

When Dylan is invited to the launch of the first Commonwealth ship made in 307 years, you can tell something will go wrong. As the ship explodes sabotage is suspected. As Dylan and the crew try to find the culprit, they encounter many different suspects while being attacked a violent pride. Can Dylan find the culprit before the Maru is next?

When an old flame of Beka's is arrested on a planet where only the truth is told, its up to the Andromeda and her crew to save the day. After repeatedly lying, Beka gets no-where so she breaks the suspect out in flees to the Andromeda. As the story unravels, it seems that all is not as it seems.....

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.

When the Andromeda responds to a request to destroy atmosphere generators on Samsarra, they encounter a battle group of Pyrians and stand off until the Commonwealth fleet arrives. in a revelation from Trance, Dylan finds out that Trances people believe the Pyrian fleet stronger and better equipped to handle the forthcoming war. With this information, she tells Dylan to pull out and let the Pyrians win so that they can take on the Magog World Ship instead of the renewed Commonwealth. Dylan sees that the only way to stop them is to destroy the planet that he is trying so hard to save....

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?

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

The Andromeda end up in the Prolon System where they discover a hibernation capsule occupied by a woman impersonating a dead princess.

The Andromeda crew search for a colony that disappeared.

When the crew prepares for the launch of The Resolution of Hector, they soon discover that Rommie has had a change of mind and is now working against the crew. Knowing that this is not normal, Dylan sets out to reclaim the ship, and find out what is controlling his friend.

When the Andromeda is attacked by the Dragons to receive the bones of Drago Mussevni something seems array. Dylan then discovers that Tyr has united all of the Neitzian people under his son, the genetic reincarnation of Drago Mussevni. Will Tyr make the right decision and help the crew of the Andromeda or lead his new people into battle?