As we start season 3 the Babylon 5 crew are presented with a new weapon with which to fight the growing Shadow threat – the first of the White Star ships. Ranger Marcus Cole joins Babylon 5. A series of random bombings rock the station and threaten the crew and the ambassadors. A group of monks from Earth arrive on the station. As G’Kar’s standing amongst the Narn is threatened, a strange alien probe approaches the station with a series of questions that have to be answered correctly within 24 hours, because otherwise Babylon 5 would be destroyed. Meanwhile Dr. Franklin struggled with his stims addiction and Garibaldi confronts him on it. Vir is assigned to Minbar as an emissary.
Then Lyta Alexander returns to Babylon 5 along with Vorlon Ambassador Kosh. Lyta is the first human to have been to the Vorlon homeworld she’s had modifications done on her by the Vorlons which better adapt her to carrying pieces of a Vorlon’s consciousness inside her. Through the use of the Great Machine, Susan Ivanova is able to inadvertently uncover new evidence that President Clark was involved in President Santiago’s assassination. This evidence is made public for the first time. Bester returns to Babylon 5 to track down a dealer of Dust, an illegal psychotropic drug that can be used as a weapon and also suggests that Talia was dissected by Vorlons. G’Kar uses Dust to telepathically assault Ambassador Mollari and learn what his role was in the war. G’Kar is sentenced to sixty days in prison for his assault.
Franklin and Marcus investigate an outbreak of parasitic aliens in Down Below. When President Clark declares martial law throughout Earth Central, the command crew must find a way to stop Nightwatch from taking over Babylon 5. Londo receives a prophecy from Emperor Turhan’s widow when she visits the station – the prophecy reveals that both Londo and Vir are destined to become Emperor. Nightwatch attempts to take over the station and is eventually rebuffed and replaced by a Narn security detail. President Clark tries to seize control of Babylon 5 by force, forcing Sheridan and the command crew to take arms against their own government. After Delenn confronts the Grey Council, Minbari ships are sent to protect the station. Vir faces calamity when his fiancée – whom he has never met – arrives on the station, and his “work” as the Centauri ambassador to Minbar is revealed. We learn more about the humans’ first encounter with the Minbari and how the war started. Bester returns to Babylon 5 and proposes a strange alliance: information on President Clark’s plans for the station in exchange for helping to liberate Shadow weapons. The Shadow War begins in earnest, and it falls to Sheridan to rally a force against them. He requests help from Kosh and it brings about profound consequences. Franklin falls further and further into his addiction.
Jeffrey Sinclair returns with a mission vital to the survival of the station: travelling back in time to steal Babylon 4. This clears up a puzzling season episode. And it is revealed that he undergoes a transformation, goes back in time and becomes known a Valen of the Minbari people. Delenn is installed as head of the Rangers, while Kosh dies and a replacement is sent. A delegation of religious leaders come to Babylon 5 to visit Brother Theo and provide assistance to Sheridan. Londo sets a plan in motion to rid himself of Lord Refa. Sheridan’s wife, who supposedly died four years ago, tries to convince Sheridan to come to Z’ha’dum and meet his opposite number. Londo receives important news about his political future. The Shadows move against Babylon 5 itself. An explosion happens on Z’hadum – is Sheridan dead?