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

In a race against Tyr to control the Route of Ages, the crew find themselves in another universe. To save them, Trance finally reveals who and what she really is.

The crew rescues two people from a spaceship, the leaders of opposing sides in a long civil war on a nearby planet. The two warring sides have built an immense wall separating the northern and southern halves of the planet, and the Northerners are suffering from a plague that is blamed on the Southerners. After Dylan contracts the plague, the crew try to assist in settling the dispute and find a cure for the plague, but nothing goes as planned.

The Collectors have been using a drug to modify people's behavior, discovering their fears in efforts to control or break them. This is their solution for dealing with Dylan. Led by a message from Rev Bem, claiming to have a weapon that can defeat the oncoming darkness, Dylan lands on a drug-trafficking planet and is soon taken captive by the Collectors.

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.

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.

The crew travels to the core of Seefra's sun Methus-2 to repair it.

As Trance's sun closes on Seefra-9, Rommie is rebuilt by Doyle to help evacuate the planet.