A Commonwealth conference becomes a backdrop for Magog espionage, while Harper tries to discover how one of their spies managed to remove some of his Magog larvae.

The crew watches Rev Bem's fairwell message, not sure whether or not to pursue him, or let him leave. Dylan says that they should respect Rev's decision to leave, but Harper snaps at Dylan and storms out. He is upset because Rev had promised to remove the Magog larvae from his gut. He writhes in pain, but when he tries to take his medication, it has no effect, as the larvae have grown immune to it, as Trance and Rev had warned him they would. Soon after, Harper enlists in Chief Technical Director Hohne's help, as well as the other Persieds. Harper plans to build a machine that will fold space to remove the eggs, but it's affecting time, as well.

The crew encounter a POW camp full of captured High Guard starships and their AI avatars.

The crew of the Andromeda meet an alien race they were destined to face.

Trance gets Beka and Dylan to medbay, while Rev goes to see a man about his god and Tyr and Harper are injected with Magog eggs and tied up. Dylan and the Andromeda avatar go down to get Tyr and Harper, leaving Beka behind with orders to use a nova bomb to detonate the "bound" planets' sun in three hours. Meanwhile Rev meets with Bloodmist, and begins to give into his bestial nature. The two of them confront the Magog "god", which seems to convince Rev to kill his friends. Bloodmist takes him to Tyr and Harper, but its a trick and Rev kills Bloodmist. Dylan and Andromeda are overwhelmed when Beka launches the nova bomb, but the Magog "god" manages to absorb all the energy. The distraction gives them time to free Tyr and Harper and get out of there. Trance manages to remove Tyr's spider eggs, but the procedure would kill Harper. He has to take medication to keep them in check, but the medicine won't work forever. Meanwhile, they've figured out that the Magog travelling "bound planets" w

Tyr learns that he is a father.

A stranger gives Dylan a message from his dead fiancée leading him to an untouched world with descendants of his former crew and friends, including the descendant of his treachorous former best friend.

After discovering Tyr has hidden the remains of Drago Musevini on board the Andromeda, Dylan questions Tyr's loyalty. Beka and a Nietzchean both race to repair their ships before the other destroys them, and Harper is left in command of the Andromeda, and must decide whether or not to protect a convoy and risk losing the Andromeda.

Rommie sets out to extract an informant, but winds up stuck on a planet with a strong hatred and fear of Androids.

The crew of Andromed encounter plague victims infected by a hostile, nanobot-based lifeform out to take over the ship.

Trance is held captive, while Dylan and the rest of the crew try to uncover the source behind mysterious attacks on cargo ships.

The crew encounter the Vedrans the long-lost founders of the Commonwealth.

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.

The crew returns for the first time to Earth, where Harper and his cousin try to save the homeworld from Nietzschean occupation.

The Andromeda is swallowed by a space creature.

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.

Teen royalty is the key to the crew quelling an alien uprising, as Dylan and Tyr become co-regents to a recently orphaned young prince.

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.

As General Burma arrives on Andromeda, with Harper in tow, Dylan and Rhade head for Methis 2, about to be crushed by Trance's sun, leaving Doyle, Rommie, and Beka to face Burma, and the forgotten enemy he brings with him.

With the help of the avatars of the nebula, the Andromeda goes through the Route of Ages, back to the Known Worlds, and the Commonwealth.

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.