Bester returns to Babylon 5 to stop the flow of Dust, a powerful new drug which can temporarily unlock telepathic powers. But Captain Sheridan and the crew can't risk Bester reading their minds and uncovering their secret Shadow war preparations.
After severing ties with Earth, the command staff must deal with some unexpected issues. Delenn suggests they go through a Minbari rebirth ceremony. Secrets are revealed, and hidden dangers are revealed as a group loyal to Clark takes Delenn hostage.
Vir returns to Babylon 5, and meets his fiancée'. As he and his bride to be get to know each other, a Narn attacks, and takes a blood oath to kill them. The command staff must figure out why someone would want to kill Vir.
Garibaldi tries to get Franklin to face up to his stim usage. Londo waits anxiously for Adira to return. Morden returns first, and manipulates the situation to his advantage. The alliance asks Sheridan to prove he has forces equal to the Shadows before they will commit. Sheridan calls on Kosh for assistance, but Kosh is resistant at first, Kosh finally agrees to help Sheridan, and later pays the price for his involvement.
Sinclair returns to Babylon 5 with a mission, going back in time to take Babylon 4 where it is most needed. This is a continuation of First Season's Babylon Squared. Many things about the past are explained. And some surprises about the future are revealed
With Sinclair gone, the Rangers need a new leader, and everyone looks to Delenn. But some in the warrior caste will not accept her in this new role, and seek a way to block her. Marcus must stop Neroon from interfering in the ceremony at any cost. Meanwhile Garibaldi investigates the death of a maintenance worker and a mysterious cult on a section that "vanished"
Religious leaders gather on Babylon 5 bringing news of events on Earth. Sheridan and Delenn figure out where the Shadows will strike next. G'Kar is captured by Refa, this will lead to a final confrontation with Londo.
Delenn asks the League for ships for a mission, she won't tell them where or when the mission will take place. The League hesitates, but they agree to support her. The fleet manages to prevent an attack by a Shadow Fleet. Franklin finally finds himself, and confronts his inner demons. An unexpected visitor from Sheridan's past arrives.
After the destruction of Z'Ha'Dum, Sheridan: presumed dead, Garibaldi: missing and the fragile alliance against the Shadows is crumbling. Mollari faces the new Emperor, and B5 is in a holding pattern, waiting for the next shoe to drop.