When Harper accidentally overrides Andromeda's personality with an older version, she hunts down the crew and goes on an old mission in which her former crew was slaughtered.

Dylan is faced with a difficult decision when Andromeda slipstreams back in time -- days before the climactic battle of the Nietzschean Revolution where the Commonwealth was defeated and the Nietzschean Alliance was destroyed.

Andromeda encounters her damaged sister ship, the Pax Magellanic, that leads the crew of the Andromeda Ascendant on an eerie mission.

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.

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?

It's the start of the war between the Systems Commonwealth and the Nietzschean fleets. Captain Dylan Hunt and his ship the Andromeda Ascendant try to flee the first Nietzschean attack to warn the Commonwealth. In his attempt to escape, the Andromeda and Captain Hunt are caught in the event horizon of a black hole and frozen in time for 300 years. The crew of the Eureka Maru with Captain Beka Valentine try to salvage the Andromeda to sell for a Nightsider's ransom. After the Andromeda is pulled free, Hunt is unfrozen and forced to defend his ship against the salvagers and the Nietzschean mercenaries lead by Tyr Anasazi.

Dylan and the crew of the Eureka Maru agree to join forces and become one team aboard the Andromeda Ascendant as they set forth on his mission to restore the Systems Commonwealth.

An arranged marriage between two rival Nietzschean Prides puts the Andromeda Ascendant in danger when Captain Dylan Hunt agrees to transport the bride to the wedding.

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?

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

"Okay, that did not work," Trance says. "Let's try again." Trance tries to figure out how to help the crew survive a deadly intruder.

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....

Rommie's emotions cause one of Harpers fail-safes to cut in, cutting her off from her core AI and shutting down all the ships systems. This creates problems, especially when a satellite ship from the Magog world ship could come out of slipstream at any moment!

The Andromeda encounters the Arkology, a society that they believe is the closest to perfection humanity will ever achieve. But the Magog are close, and Dylan and the crew must convince the utopia that peace is not the answer. Conflict arises in the core crew when the leaders of Arkology do not wish to leave. Dylan wants to defend them, and Beka warns him that she's not going to stay and die defending an idea of peace.

As the Nietzschean fleet approaches, the Andromeda prepares for the final battle.

Captain Dylan Hunt must save the Andromeda from the Nietzscheans, who are trying to persuade Tyr to help them destroy the ship and rebuild his Nietzschean life. His new life would include a wife to carry on his lineage.

Finally, after 300 years and a black hole keeping them apart, Captain Dylan Hunt reunites with his true love, Sara.

Harper finds himself overloaded with information when a dying Perseid transfers data into his brain.

The reappearance of Tyr Anasazi and Telemachus Rhade leads to a race to obtain the Route of Ages, which will direct the owner to the location of the Abyss itself. Dylan and the crew plan to use it as a weapon, while Tyr plans on bargaining with the Abyss in hopes of it sparing his empire.

While on a mission on the Maru, Dylan, Rhade and Harper (and the Maru) are captured by the Templars. The Patriarch of the Templars presses Harper to help him build a bridge -- a time bridge to 210 years in the future. However, sometimes even the future is unpredictable. Meanwhile, Beka, Trance and Rommie chase down smuggler ships.

Beka decides to leave the crew to fight for themselves, but after all of the promises that everyone will be reunited, Trance tells them that they will never be as they are again. When the Magog Worldship finally re-encounters the Andromeda after two years, Rommie and Harper race to take the Arkology to slipstream, Rhade must teach the inhabitants to defend themselves, and Dylan and Trance fight off the invading Magog. But as the Andromeda becomes covered in swarmships, Trance tells Dylan that he--and only he--may escape this alive.

Tyr and Rommie are framed for the assassination of the Castalian president.

A crash landing on a strange planet leaves Tyr with a complete loss of memory and a mystery crate to protect from not-so-brotherly Nietzcheans.

Rev Bem gets a call from a Wayist friend in need of his help to save the Hajira and its settlement, Serendipity, from being taken over by slavers.

Rommie falls in love with a surviving android (Michael Shanks) of a destroyed ship, only to be betrayed as he turns out to be the ultimate enemy.