The actors were never told in advance what was in store for their characters. Each new episode was just as much a surprise for them as it was for the viewers.　　故事的背景设定在公元2257年，人类已经突破光速，开始大规模星际旅行及在太阳系附近殖民，与多个外星文明接触并有贸易联系。一天，一艘地球联邦的星际驱逐舰在探索未知星际空间的时候遇到一艘不明星船，因为误判对方意图而先敌开火。对方叫明巴利外星族（Minbari），比人类早进化发展几千年，其技术人类无法望其项背。不巧的是地球星船孤注一掷先敌开火的时候把灰色議會議長杜哈的给干掉了（那位老兄其实知道按大设计蓝图，明巴利必须与地球人联合并融合，这次到这里也不是闲逛，而是准备与地球人第一次亲密接触）。于是明巴利对地球开战，摧枯拉朽所向披糜，在对地球本土最后一击的过程中，明巴利却突然停止进攻并宣布投降。总之，停战后地球出资在中立空间建设“巴比伦空间站"，致力星际交流、谈判及和平合作。前面四座都被摧毁或莫名其妙消失，于是有了巴比伦5号。巴5军头Sheridan和明巴利大使笛嵐（Delenn）带领众喽罗，联合火星殖民地抵抗力量反对地球联邦通过谋杀政变而上台的独裁总统，联合各外星文明反击神秘黑暗种类——影族（Shadows），向佛隆人（Vorlon）说不，最终走上独立自主自力更生的发展文明道路。

　　At the beginning of 2259, Captain John Sheridan replaces 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 the Psi Corps, an increasingly autocratic organization which oversees and controls the lives of human telepaths. 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 Ambassador Londo Mollari unknowingly enlists their aid through his association with the mysterious Mr. Morden in 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 the 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 a full-scale war breaks out, the Centauri eventually conquer Narn in a brutal attack involving mass drivers, outlawed weapons of mass destruction. Towards the end of the year, the Clark administration begins to show increasingly totalitarian characteristics, clamping down on dissent and restricting freedom of speech. The Vorlons are revealed to be the basis of legends about angels on 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 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 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 (the First Ones) to their cause, against both the Shadows and the Vorlons. Captain John Sheridan returns to the station after escaping from 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 and returned 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 Emperor Cartagia forges 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 the Centauri homeworld, in an attempt to save 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 the Vorlons and 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". He begins working for one William Edgars, a Mars Tycoon, who is married to Garibaldi's former love. While he works ever closer with Edgars, he becomes increasingly aggressive towards Sheridan and eventually leaves Babylon 5.　　Minbar is gripped by a brief civil war between the Warrior and Religious castes. Delenn secretly meets with Neroon of the Warrior caste and convinces him that neither side can be allowed to win. She tells him that she will undergo a ritual wherein she will be willing to sacrifice herself, but will stop the ritual before she actually dies. When Neroon sees that she actually intends to go through the entire ritual, he rescues her and sacrifices himself instead, declaring that, although he was born Warrior, in his heart he is Religious.　　As part of the ongoing conflict between Earth and Babylon 5, Garibaldi eventually betrays Sheridan and arranges his capture in order to gain Edgars' trust and learn his plans. Garibaldi later learns that Edgars created a virus that is dangerous to only telepaths. It is then revealed, that 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. Bester releases Garibaldi of his programming, and allows him to remember everything he has done since being kidnapped. Edgars is killed and his wife disappears, but is reunited with Garibaldi after the end of the war. Garibaldi helps 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 resign his commission. The League of Non-Aligned Worlds is dissolved and reformed into the Interstellar Alliance, with Sheridan elected as its first President and continuing his command of the Rangers, who are to act as a galactic equivalent of United 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 a pre-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 goes nova.

　　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.