The five seasons of the series each correspond to one fictional sequential year in the period 2258–2262. Each season shares its name with an episode that is central to that season's plot. As the series starts, the Babylon 5 station is welcoming ambassadors from various races in the galaxy. Earth has just barely survived an accidental war with the powerfulMinbari, who, despite their superior technology, mysteriously surrendered at the brink of the destruction of the human race (theBattle of the Line).
During 2258,Commander Jeffrey Sinclairis in charge of the station. Much of the story revolves around his gradual discovery that it was his capture by the Minbari at the Battle of the Line which ended the war against Earth. Upon capturing Sinclair, the Minbari came to believe thatValen, a great Minbari leader and hero of the last Minbari-Shadow war, had been reincarnated as the Commander. Concluding that others of their species had been, and were continuing to be reborn as humans, and in obedience to the edict that Minbari do not kill one another, lest they harm the soul, they stopped the war just asEarth'sfinal defenses were on the verge of collapse.
It is gradually revealed thatAmbassador Delennis a member of the mysterious and powerfulGrey Council, the ruling body of the Minbari. Towards the end of 2258, she begins the transformation into a Minbari-human hybrid, ostensibly to build a bridge between the humans and Minbari. The year ends with the assassination ofEarth AlliancePresident Luis Santiago, and rising tension between the Narn and Centauri, after a Narn outpost is completely destroyed by an unknown third party.
At the beginning of 2259,Captain John Sheridanreplaces Sinclair as the military governor of the station. He and the command staff learn that the death of President Santiago was actually an assassination masterminded by Vice President Clark (who assumed the Presidency upon Santiago's death). A conflict develops between the Babylon 5 command staff and thePsi Corps, an increasinglyautocraticorganization which oversees and controls the lives of humantelepaths. Commander Ivanova, the second-in-command of the station, is secretly a latent telepath who has illicitly avoided registering with the Psi Corps.
The Shadows, an ancient and extremely powerful race who have recently emerged from hibernation, are revealed to be the cause of a variety of mysterious and disturbing events, including the attack on the Narn outpost at the end of 2258. Centauri AmbassadorLondo Mollariunknowingly enlists their aid through his association with the mysteriousMr. Mordenin the ongoing conflict with the Narn. The elderly and ailing Centauri emperor, long an advocate of reconciliation with the Narn, dies suddenly while visiting Babylon 5. A number of conspirators, including Londo Mollari and Refa, take control of Centauri government by assassinating their opponents and placing the late emperor's unstable nephew on the throne. Their first act is to start open aggression against the Narn. After full-scale war breaks out, the Centauri eventually conquer Narn in a brutal attack involvingmass drivers, outlawedweapons of mass destruction. Towards the end of the year, the Clark administration begins to show increasingly totalitarian characteristics, clamping down on dissent and restrictingfreedom of speech. TheVorlonsare revealed to be the basis of legends aboutangelson various worlds, including Earth, and are the ancient enemies of the Shadows. They enlist the aid of Sheridan and the Babylon 5 command staff in the struggle against the Shadows.
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 increasinglyxenophobicand totalitarian, and uses a military incident as an excuse to declare martial law. This triggers a war of independence onMars, 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. 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 ambassadorKosh Naranekinto launching an attack against their mutual enemy. Kosh's deeds lead to his subsequent assassination by the Shadows.
Upon returning to the station, former commander Jeffrey Sinclair enlists the aid of Captain Sheridan, Delenn, Ivanova and Marcus and convinces them to help him steal theBabylon 4space station, intending to send it back in time 1,000 years to use it as a base of operations against the Shadows in the first 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 toZ'ha'dum, the Shadow homeworld, in an attempt by them to recruit him. However he instead destroys their largest city in akamikazenuclear 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 2261, the Vorlons join the Shadow War, but their tactics become a concern for the alliance when the Vorlons begin destroying entire planets which they deem to have been "influenced" by the Shadows. Disturbed by this turn of events, Babylon 5 recruits several other powerful and ancient races (theFirst Ones) to their cause, against both the Shadows and the Vorlons. Captain John Sheridan returns to the station after escaping the destruction of Z'ha'dum, but at a price: barring illness or injury, he has only 20 years left to live. He is accompanied by a mysterious alien named Lorien who claims to be the oldest sentient being in the galaxy.
Hours before Sheridan's return, Garibaldi is rescued back to the station, in rather dubious circumstances. He is markedly more paranoid and suspicious of other alien races and of Sheridan than he was before.
Centauri EmperorCartagiaforges a relationship with the Shadows. Londo Mollari engineers the assassination of Cartagia and repudiates his agreement with the Shadows. Londo kills Mr. Morden and destroys the Shadow vessels based on theCentauri homeworld, thus saving his planet from destruction by the Vorlons. Aided by the other ancient races, and several younger ones, Sheridan lures both the Vorlons and the Shadows into an immense battle, during which theVorlonsand Shadows reveal that they have been left as guardians of the younger races, but due to philosophical differences, ended up using them as pawns in their endless wars throughout the ages. The younger races reject their continued interference, and the Vorlons and Shadows, along with the remaining First Ones, agree to depart the galaxy forever.
After the Shadows are defeated Garibaldi leaves his post as security chief and works on his own as a "provider of information". Garibaldi was actually abducted by the Psi-Corps at the end of Season 3 and re-programmed by Bester to provide information to him at the right time.
Minbaris gripped by a brief civil war. Garibaldi betrays Sheridan and arranges his capture. Garibaldi later reveals to Bester about a virus that is dangerous to only telepaths, which the Psi-Corps then destroys. Bester releases Garibaldi of his programming, and allows him to remember everything he has done since being kidnapped. Garibaldi helps to free Sheridan and return him to the campaign to free Earth. An alliance led by Babylon 5 frees Earth from totalitarian rule by President Clark in a short but bloody war. This culminates in Clark's suicide and the restoration of democratic government. Mars is granted full independence, and Sheridan agrees to step down as commander of Babylon 5. TheLeague of Non-Aligned Worldsis dissolved and reformed into theInterstellar Alliance, with Sheridan elected as its first President and continuing his command of theRangers, who are to act as a galactic equivalent ofUnited Nations peacekeepers.
In the season finale, the events of 100, 500, 1000, and one million years into the future are shown, depicting Babylon 5's lasting influence throughout history. Amongst the events shown are the political aftermath of the 2261 civil war, a subsequent nuclear war on Earth involving a new totalitarian government in the year AD 2762, the resulting fall of Earth into apre-industrial society, the loss and restoration of humanity's knowledge of space travel, and the final evolution of mankind into energy beings similar to the Vorlons, after which Earth's sun goesnova.
In 2262, Earthforce CaptainElizabeth Lochleyis appointed to command Babylon 5. The station grows in its role as a sanctuary for rogue telepaths running from thePsi Corps, resulting in a violent conflict.G'Kar, former Narn ambassador to Babylon 5, becomes a spiritual leader after a book was published that he wrote while incarcerated during the Narn-Centauri War. TheDrakh, former allies of the Shadows who remained in the galaxy, take control ofRegentVirinion 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 consequently decimated byNarnandDraziwarships, 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 time-travel sequences throughout the series; one such sequence shows Mollari and former nemesis (and later friend) G'Kar dying at each other's throats in an act of mutual suicide.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.
Twenty years later, on the verge of death, Sheridan takes one final trip to the now-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. The Babylon 5 station is completely destroyed in a planned demolition shortly after Sheridan's departure, its existence no longer necessary as the Alliance has taken over its diplomatic purposes.