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.
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.
The death of a man from Beka's past named Weslow, sends the crew in search of an archive that can let Beka relive some of her childhood experiences so that she may make sense of Weslow's dying words.
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!
While the Andromeda is confronted by the Commonwealth fleet and Tri-Jema, Dylan must decide whether or not he can entrust the Route of Ages to them.
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.
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.
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.
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.
One of Harper's experiments goes awry, and Dylan ends up in an alternate reality.
The crew intercepts a mysterious cargo en route to a war zone.
Dylan is put on trial for high crimes against the Commonwealth.
The crew searches for a princess abducted by a ruthless pirate. As usual, nothing is as it seems. Along the way, a secret from Beka's past is revealed.
Harper attends a conference of the Commonwealth's greatest minds. Unfortunately, a mysterious assassin has plans for that collected brilliance. Meanwhile, Dylan is being escorted to meet with Tri-Lorn... or is he?
The crew assists in the search for escaped prisoners on a new Commonwealth member world. Dylan finds himself playing a role in an ancient prophecy.
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 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.
The ultimate weapon falls into the hands of a Nietzschean pirate. Can Harper disarm it before the Magog arrive?
Dylan plays a dangerous game against two gamblers, but not everything is as real as it seems.
Dylan and an old friend try to prevent the maker of the Magog Worldship from deploying an army of androids.
A power-hungry citizen seeks to manipulate the Commonwealth for his own gain. Dylan receives an unsettling view of his future from a prophetic alien.
A seemingly psychotic ""Collector"" simultaneously takes credit and blames Dylan for the fall of the Commonwealth. He also claims to be hosting (or holding captive?) the Triumvir Tri-Jema. The crew must decide whether to accompany Dylan on yet another odds-defying journey to save the Universe or to retire in relative safety.
