The Psi Corps and President Clark, whose government has discovered Shadow vessels buried in Earth's solar system, begin to harness the vessels' advanced technology. The Clark administration continues to become increasingly xenophobic and totalitarian, and uses a military incident as an excuse to declare martial law. This triggers a war of independence on Mars, which had long had a strained political relationship with Earth. Babylon 5 also declares independence from Earth, along with several other outlying Earth Alliance colonies. In response, the Earth Alliance attempts to retake Babylon 5 by force, but with the aid of the Minbari, who have allied with the station against the growing Shadow threat, the attack is repelled.
Becoming concerned over the Shadows' growing influence amongst his people, Centauri ambassador Londo Mollari attempts to sever ties with them. Mr. Morden, the Shadows' human representative, tricks him into restoring the partnership by engineering the murder of Mollari's mistress while putting the blame on a rival Centauri House. Open warfare breaks out between the Shadows and the alliance led by Babylon 5 and the Minbari. It is learned that genetic manipulation by the Vorlons is the source of human telepathy, as it is later discovered that Shadow ships are vulnerable to telepathic attacks. Displeased at the Vorlons' lack of direct action against the Shadows, Captain John Sheridan browbeats Vorlon ambassador Kosh Naranek into launching an attack against their mutual enemy. Kosh's deeds lead to his subsequent assassination by the Shadows.
Former station commander Jeffrey Sinclair returns to Babylon 5 to enlist the aid of Captain Sheridan, Delenn, Ivanova and Marcus in stealing the Babylon 4 space station and sending it 1,000 years back in time to use it as a base of operations against the Shadows in the previous Minbari-Shadow war. Undergoing the same transformation as Delenn at the end of Season 1, Sinclair transforms into a Minbari and is subsequently revealed to be the actual Valen of Minbari legend, rather than a reincarnation. Spurred by the reappearance of his assumed-dead wife (who now works for the Shadows), Sheridan travels to Z'ha'dum, the Shadow homeworld, in an attempt by them to recruit him. However he instead destroys their largest city in a kamikaze nuclear attack, and is last seen jumping into a miles-deep pit to escape the explosion. Garibaldi, during a fight with Shadow vessels, goes missing.
In 2262, Earthforce Captain Elizabeth Lochley is appointed to command Babylon 5. The station grows in its role as a sanctuary for rogue telepaths running from the Psi Corps, resulting in conflict. G'Kar, former Narn ambassador to Babylon 5, becomes unwillingly a spiritual icon after a book is published that he wrote while incarcerated during the Narn-Centauri War. The Drakh, former allies of the Shadows who remained in the galaxy, take control of Regent Virini on Centauri Prime through a parasitic creature called a Keeper, then incite a war between the Centauri and the Interstellar Alliance, in order to isolate the Centauri from the Alliance and gain a malleable homeworld for themselves.
Centauri Prime is devastated by Narn and Drazi warships and Londo Mollari becomes emperor, accepting a Drakh Keeper under threat of the complete nuclear destruction of the planet. (Portions of the end of his reign are seen in various prescient visions throughout the series; they show Mollari and former nemesis (and later friend) G'Kar sixteen years in the future dying at each other's throats, seemingly out of their grudge. It is gradually revealed that there was a much more friendly subtext, with Mollari having become a slave to the drakh rule and being tired of life; his Drakh Keeper awakens and strangles G'Kar in return. Vir Cotto, Mollari's loyal and more moral aide, succeeds him as emperor, free of Drakh influence. Sheridan and Delenn marry and move to Minbar, along with the headquarters of the Interstellar Alliance. G'Kar leaves Babylon 5 to escape his unwanted fame and explore the rim. Garibaldi also marries and settles down on Mars. Most of the other main characters leave B5.
Nineteen years later on the verge of death, Sheridan takes a final trip to the obsolete Babylon 5 station before its decommissioning. Sheridan apparently dies but is claimed by the First Ones, who invite him to join them on a journey beyond the rim of the galaxy. Babylon 5 station is destroyed in a demolition shortly after Sheridan's departure, its existence no longer necessary as the Alliance has taken over its diplomatic purposes. This final episode features a cameo by Straczynski as the technician who switches off the lights before Babylon 5 is demolished.
