It is now the year 2259. Five hostile federations dominate the outermost regions of space. This season, Babylon 5's captain declares the station an independent state and forms a war council to battle the evil Shadows – and their allies on Earth.
An Earthforce investigator comes to B5 with Lt. Keffer's last recording, asking the ambassadors if they recognize the ship in it. Meanwhile Londo takes steps to remove himself from the Shadows, and Sheridan takes the White Star out for its first mission.
A bomber is loose on Babylon 5; setting of bombs with seemingly no pattern. G'Kar blames the Centauri, Londo blames the Narn - and in it all, Lennier is critically injured. At the same time a group of monks request permission to live on the station.
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.
One of the monks starts having disturbing visions and realizes that his past may not be how he remembers it. Meanwhile Lyta causes a bit of commotion when she returns from the Vorlon homeworld.
Delenn decides its time to try to contact some of the first ones and enlists the help of Draal, while Babylon 5 is assigned a political officer.
Bester comes to the station to track down a dealer of Dust - an illegal drug that gives normal people temporary telepathic powers. G'Kar is also interested in the drug. He sees it as a potential weapon against the Centauri, but first he has to test it...
Marcus starts snooping around Downbelow when some of his contacts start behaving unusually and a lurker is found dead with a strange creature bonded to his spine. Ivanova investigates Corwin's loyalties when he receives a promotion.
An archeologist is brought Babylon 5 with a grave massage - a dormant Shadow ship has been found on Ganymede. It must be destroyed before it falls into the hands of President Clark.
Clark has just declared marshal 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.
The renegade destroyer ""Alexander"" arrives at Babylon 5 and Sheridan is forced to announce the station's secession from the Earth Alliance, and prepare for an attack by Clark's forces. Meanwhile Delenn is forced to go to Minbar when the Grey Council refuses to act upon increased Shadow activity.
Delenn prepares for a ceremony of rebirth, the station's computer goes through an interesting change, Londo "encourages" Refa to stop associating with the Shadows, and the remains of the Nightwatch on Babylon 5 plan to strike at Sheridan through Delenn.
Vir returns to Babylon 5 to find that he now has a wife and that two Narns are out for his blood. Meanwhile Ivanova investigates the activities of the mysterious Centauri Abrahamo Linconi.
A mysterious man comes to Babylon 5 dressed in chainmail and armed with a sword. His name? King Arthur - Son of Uther Pendragon, come to help when he is needed most.
Bester comes to Babylon 5, this time seeking help against a common enemy - the Shadows. Meanwhile G'Kar demands to be included in the War Council.
Morden returns to secure Londo's cooperation again, Garibaldi confronts Franklin about the stims and Kosh gives Sheridan a victory against the Shadows - but at a price.
Ivanova gets a distress call from herself pleading for help as the Shadows destroy Babylon 5. It is dated eight days into the future. At the same time, on Minbar, Sinclair is given a nine-hundred-year-old letter from Valen, telling him that a drastic action must be taken to prevent that future.
While Sheridan is unstuck in time, seeing a glimpse of a future Centauri Prime in ruins, the others continue with their plan to take Babylon 4 back in time.
The new Vorlon ambassador arrives, Sheridan decides it's time to test just how effective telepaths are against the Shadow ships, and Franklin is on walkabout in Downbelow and falls in love with a singer.
Garibaldi investigates an area where a maintenance worker disappeared and finds a whole floor that was forgotten after construction, including its rather strange inhabitants. Meanwhile Delenn is about to take on the role of Ranger One, but Neroon swears to stop her.
Londo forces Vir to participate in a plan to kill G'Kar. Sheridan struggles with figuring out the Shadows' tactics.
With the Shadows next target known, a massive counterattack is prepared. Ivanova and Marcus scout ahead in the White Star, while the fleet stands by in hyperspace. At the same time, Franklin finally has to face his problems as he lies fatally wounded in Downbelow.