This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "Whatever Happened to Mr. Garibaldi?." Note that this is chock full of spoilers!
Thirteen years ago, humanity teetered on the brink of extermination after a misunderstanding mobilized the entire Minbari civilization on a mission of annihilation. The Babylon Project was Earth's attempt to prevent future interstellar war by promoting interracial understanding. It failed utterly. A galactic war of epic proportions engulfed Babylon 5 only five years after its completion. In the face of overwhelming darkness and chaos, the people of B5 found the courage to make a stand against madness and despair. Yet the price was enormous. They lost their homes, their loved ones, their careers -- even their lives.
The Great War is the handiwork of the Shadows. An ancient, terrifyingly powerful race, the Shadows seed the galaxy with chaos like cosmic picadors, promoting evolutionary advancement through competition and destruction. A thousand years ago they were beaten back to the galactic rim by an alliance which included relatively young civilizations like the Minbari, and a number of extremely powerful older races known collectively as the First Ones. Of these, all but the Vorlons have passed beyond confines of the galaxy -- presumably forever. The Shadows have infiltrated several governments, preferring secrecy because in the open their organic vessels have one crucial vulnerability: they can be disabled by telepaths. Although forced on the defensive when Captain Sheridan destroyed the biggest city on their home world of Z'ha'dum, the Shadows have no intention of giving up their goals easily, whatever those goals might ultimately be.
The Shadows' greatest remaining enemies are the Vorlons. Enigmatic, secretive and extremely powerful, the Vorlons have also manipulated many civilizations for their own mysterious ends. Their sole acknowledged representative, Ambassador Kosh Naranek, glided the corridors of B5 for years before anyone saw him outside his bulky encounter suit. When he finally revealed himself, he appeared as a glorious being of light and lore, of the same species as any who saw him.
Only one individual is known to have ever visited the Vorlon homeworld, the human telepath Lyta Alexander. When she returned to act as aide and "courier" for Ambassador Kosh, she had obviously been altered. Besides Lyta, Kosh took an interest in Delenn, to teach, test and trust her. But his most curious relationship was reserved for Captain Sheridan, who he pushed and taught and chastised. Finally when Sheridan demanded that the Vorlons take part in the war they were commanding him to fight for them, Kosh acquiesced at the cost of his own life -- or at least most of it. Even as the Shadows destroyed the Ambassador in retribution, a small piece of Kosh's consciousness slipped into the Captain to guide his path in the future.
The replacement Ambassador, also known as "Kosh," is more remote and more clearly working toward ends that include no one but Vorlons.
In the declining years of the great Centauri Empire, the Shadows' human puppet, Mr. Morden, approached a debauched, washed-up, old Centauri patriot, Londo Mollari, and offered him the chance for his people to regain their lost might and glory. In exchange Morden asked... well, nothing, at first. Londo took the bait and presided over the reconquest of Narn. The star of House Mollari soared, but Londo felt that circumstances were flying out of control. The machinations of his ally-turned-enemy Lord Refa, the urgings of Mr. Morden's "associates" to wage excessive and pointless border wars, the rudderless court at home, and his own desire to serve his people, all pushed the Ambassador into a newly decisive role. Yet, tragically it appears that it will be his destiny to lead his people into ruin and desolation.
When G'Kar first came to Babylon 5, he was a hero who had spent his entire life fighting the Centauri. His hatred and fury knew no limits, and thus he ironically provided the perfect target for Londo's temptation by the Shadows. When his world was defeated, G'Kar was forced to beg sanctuary from Babylon 5 and there he became the leader of the Narn resistance in exile. G'Kar discovered the Shadows' return long before it became widely known, but his warnings fell on seemingly deaf ears. Eventually he learned the terrible truth: that Londo had masterminded the Shadow destruction of his people, and that the Minbari and the Army of Light had known this, and permitted it to happen. In the very instant of such revelations he experienced a Vorlon-inspired epiphany: "Some must be sacrificed if all are to be saved." He came to understand as well that somehow the humans would be the key to the salvation of his people.
While reports from "back home" had never been wildly encouraging, including the crushing of the Mars Independence movement and the Gestapo-like Nightwatch division of the Ministry of Peace, the B5 command staff were still appalled when they stumbled across evidence that President Clark had had his predecessor assassinated. When this news leaked to the press, Clark disbanded the government and declared martial law. Even as his loyal forces hunted down rebellious ships and bombed civilian targets, Mars, Io and Babylon 5 declared their independence. With Minbari assistance, B5 held off a massive Earth assault. This success left the station floating in uneasy limbo, dependent on the goodwill and self-interest of worlds who might want to use it for trade and peace negotiations.
Believing themselves to be the next evolutionary step beyond "normals," members of Psi Corps have consistently shown disregard for the laws intended to regulate their activities, along with disregard for the rights and well-being of other telepaths. They hound rogue teeps to the ends of the galaxy; they plant personality time bombs in their members as they did to Talia Winters; they develop and distribute dangerous psi-enhancing drugs like "dust;" and some within the Corps are even willing to hand over rebellious telepaths to the Shadows. They manipulate, coerce, conspire and league with the devil in pursuit of one goal -- control. However, even within an organization so guarded, there are signs of dissent and factionalization. In his anger over the ill-treatment of his lover, one of the Psi Corps' strongest telepaths, Alfred Bester, has promised to lend his aid to the station in their fight against the Shadows.
As prophesied by Valen, the Great War has brought the Minbari to the close of an age, ending a thousand years of peaceful rule by the Grey Council. Council member for the religious caste, Delenn was among the few who understood and believed the many prophecies about this time. Thus she was one of the few prepared for the terrific consequences and sacrifices required by those prophecies as one by one they came true.
The first was over a decade ago, in the terrible hour when the Grey Council war cruiser poised over Earth in a final lull before exacting ultimate vengeance for their leader Dukhat's death. A lone pilot, Jeffrey Sinclair, was captured and interrogated. To their horror, the Council discovered that he carried the soul of their greatest leader, Valen, and determined that Minbari souls were being reborn in the bodies of humans. They immediately and without explanation ordered their forces to surrender, to the outrage of the warrior caste.
The ancients said that the two halves of the Minbari soul must join to overcome their greatest challenge. They also spoke of a great leader. Believing that she was this person, Delenn underwent a metamorphosis that left her half human -- and ostracized by both races. She rose to the challenge, however, and when the Grey Council, which had been established to guard against the Shadows' return, balked when the circumstances of that return announced themselves as interspecies border conflicts, Delenn broke the Council and led the worker and religious castes into battle. This threw the tightly knit society into a turmoil, with Delenn in the unrelished middle of it all.
The Great War never ends, it just stops for awhile. It is the war that Commander Sinclair/Valen and Babylon 4 traveled backward through time to win a thousand years ago. It is the Great War prophesied to play out again in another thousand years.
Bloody though it was, the Minbari War certainly hadn't prepared the successful, patriotic, young Captain Sheridan for the task of commanding Babylon 5, much less the hardships which followed. Trying to steer a path between the political, the practical, and the ethical would have been impossible if not for his able and like-minded command staff: Ivanova, Garibaldi and Franklin. Initially these four came together to fight the darkness growing within Earth Gov, but soon they found that this evil was only a piece of the terrifying storm brewing, and they were too few alone.
The first to join the Army of Light were the crack Minbari-human battalion known as Rangers. Then, through persuasion, coercion and a show of arms, Sheridan was able to hammer together a fragile Alliance that included many of the Non-Aligned Worlds, and Delenn's two thirds of the Minbari. He also found some unexpected allies, including Draal, the sentient heart of the great machine below the station on Epsilon 3; the ancient, First One Walkers of Sigma 957; remnants of the Earth Force resistance against President Clark; and a promise from Psi Cop Mr. Bester.
When the Alliance scored a major victory over the Shadows at last, the enemy grew afraid. They sent Anna Sheridan, who they had captured with Mr. Morden from the Icarus expedition, to summon John to Z'ha'dum. Even though Kosh had warned him that he would die, and he knew it was a trap, Sheridan went there anyway and destroyed their greatest city before plunging to certain death in an immense chasm.
G'Kar set out in search of Garibaldi, who was taken by a Shadow ship during Sheridan's confrontation with the Shadows, in "The Hour of the Wolf." Londo took up a position in the royal court, but soon discovered that the Emperor was insane and had made a deal with the Shadows in the belief that they would elevate him to godhood. A rescue mission was mounted to Z'ha'dum, but Sheridan was nowhere to be found. Somehow, though, he survived, and found himself at the bottom of the chasm accompanied by an enigmatic alien.