While leading a Starfury squadron to investigate the disappearance of several ships, Sheridan is captured by an alien vessel. Meanwhile, Delenn is summoned to appear before the Grey Council to discuss her recent change in appearance.

The new Centauri appointed Narn government send a replacement for G'Kar, while an alien probe threatens to destroy Babylon 5 unless it gets the answers for a series of complicated scientific questions.

Clark has just declared martial law, and while Nightwatch prepare to take control of the station, Zack has to decide whose side he's on. In an exercise of bad timing, the prophetic widow of emperor Turhan finally comes to the station, granting Londo the visit he's been begging her for, for a long time.

It looks like the Alliance will get a break in the investigation of the recent shipping line attacks, when a possible witness may have survived the latest attack and taken refuge on the Drazi homeworld. Garibaldi is sent to find him, but the Intelligence Chief's alcohol problem complicates the mission. G'Kar returns to Babylon 5 to discover that his book has been published, and he is now a revered religious figure.

It is near the end of 2262, and many changes are abound. Londo, G'Kar and Garibaldi have already left, and Franklin will be taking up his new position on Earth shortly. Finally, Sheridan and Delenn leave for Minbar, where the Alliance's recently finished headquarters are located.