Beka and Tyr square off against Dylan for leadership of Andromeda during a dangerous face-off with an unknown enemy.

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.

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.

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.