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"
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.
