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.

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.

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 crew of the Andromeda replaces a sacred relic with a fake, attempting to negotiate peace between two battling parties.

Dylan hijacks a starship to lose the Ogami.

Beka, Dylan and Trance attempt to find the Engine of Creation, an artifact able to rearrange space and time.

Dylan, Beka, Rev Bem and Tyr pursued by a gang of Neitzscheans, are forced to make a crash landing on an icy planet.

Hunting for the woman who set up the only major interstellar alliance since the Fall, Dylan finds himself in a bar at the edge of a desert wasteland, trying to fend of a Kalderan attack.

As an old friend of Beka's has died, she tells the crew about her past.

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.