A small colony is attacked by the Shadows. It's the location of a Ranger training base, Marcus Cole goes to Babylon 5 to get help. Sheridan and Delenn embark on a mission to help the Rangers in the newly built White Star. Meanwhile Earth force sends a representative to find out more about the ship that destroyed Lt. Keffer.
A mad bomber is loose on Babylon 5. When they find him, he threatens to detonate the station, if his demands are not met. Meanwhile G'Kar and Londo are trapped in an elevator. Londo wants to work together so they can escape, but G'Kar refuses to aide his nemesis.
Sheridan and Ivanova deal with a dispute with the worker's guild. Then a probe arrives, and gives the station a test. If they pass, it promises to share advanced technology, if they fail the station will be destroyed in a few hours. Garibaldi talks to Franklin about his stim use-age.
Kosh's ship arrives at the station bearing a surprise visitor, Lyta Alexander returns after visiting the Vorlon home world. Brother Edward, a monk with Brother Theo visits with Delenn to discuss religion. Soon he begins to hear voices. They discover that Edward is experiencing repressed memories, someone is forcing him to relive past moments. Why would someone make a monk relive such horrors?
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.