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。
2244年年底，地球联盟军方派遣以詹考斯基舰长（Captain Jankowski）指挥的普罗米休斯号（Prometheus）巡洋舰为首的武装探测舰队前往明巴利边境进行军事情报侦搜，在完成最后一次的跳跃航行后，地球联盟舰队进入明巴利边境；此时，前往札哈洞的明巴利舰队也离开了最后一个边区哨站，当时的明巴利战舰上正在举行灰色议会新成员笛岚（Delenn）的入会仪式，由议长杜哈亲自主持。
詹考斯基舰长发现明巴利舰队的踪影，而明巴利战舰的人员也发现了地球联盟的武装探测舰队，双方相互侦测，但地球联盟方面因为科技远落后于明巴利，以至于无法锁定明巴利人的船舰，詹考斯基舰长决定发出讯息：我们只是来进行探测的，我们并没有恶意。同时，明巴利人也收到了这则通讯，但因为语言不通无法取得有效联系，因此明巴利军方决定依照传统，打开战舰上所有的炮门，以示我方的军容盛大与挚的待客礼仪，但是，詹考斯基却误会这项传统仪式，认为这是明巴利人恶意而不友善的举动，便决定先发制人。
这场因误会而起的冲突造成了灰色议会议长杜哈的身亡，灰色议会顿时分裂成主战与主和两派，新成员笛岚感于与杜哈的友谊与提携，在悲伤与盛怒之下投下关键性的一票：追踪敌方舰队展开复仇圣战。
这场战争自开打起，人类就一直处于绝对的劣势，一场小小的胜利都没有尝过，此时，地球联盟军方深刻了解到两件事情：第一，我们需要一场重大的胜利来激励士气以扭转战局；第二，要是无法有效反败为胜，那人类只有走向灭绝一途。
唯一的一场胜仗是由约翰薛瑞登少校（Lt. Commander John Sheridan）所指挥的莱辛顿号（Lexinton）在小行星带设下战术热核炸弹陷阱，以假的求救讯号引诱明巴利旗舰黑星号（Black Star）进入热核炸弹引爆范围而成功摧毁之。
也因为这场胜利的激励，人类在这场战争苦撑了两年之久，在2247年底，明巴利人终于迫近人类的故乡：地球。在最后的地球保卫绝战的前夕，地球联盟的总统号召全体人类共同为了人类的延续做最终的圣战与奉献，只要能够多拖延敌方一分钟，就会有更多的人们逃往中立区以延续人类的文明命脉。
人类组成史上前所未有的战斗队伍进行这场殊死地球保卫战，双方在月球轨道附近形成惨烈的战线（The Battle of the
Line），人类整体还是居于挨打的地位；但是，就在明巴利舰队即将胜利的前一刻，明巴利人突然宣布投降，而这个突如其来的投降却困扰整个宇宙长达十年之久。
"转自星际之门中文网 SGT字幕组出品"
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.
