This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "Passing Through Gethsemane." Note that this is chock full of spoilers!
The Babylon Project was conceived by the Earth government in the aftermath of the Earth-Minbari War. It was finally realized in Babylon 5, a diplomatic outpost created to promote peaceful conflict resolution. Even with such lofty goals, its galactic significance has quickly outstripped its founders' wildest dreams -- let alone their ability to control. Babylon 5's early years have been marked by a growing sense of foreboding, punctuated by successively more immediate threats to the station's safety. Yet as rising darkness nurtures galaxy-wide despair, the station begins to become the focal point for a number of tiny rays of light.
The gloom is made incarnate by the return of a mysterious ancient race known only as the Shadows. A thousand years ago they were beaten back to the rim of known space 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, who with the exception of the Vorlons have all passed beyond the confines of the galaxy -- presumably forever. On the rim, on dead deserted worlds like Z'ha'dum, the Shadows hid and gathered their strength for another assault ("In the Shadow of Z'ha'dum.") They do not act openly yet, but only through proxies like the human Mr. Morden, and the Centauri. What do they want? Only they know for sure. Chaos, it would seem, and control, and about two thirds of the galaxy.
It is ironic for a people as dedicated to hedonism and frivolity as the Centauri to become the facilitators of destruction and despair. Yet they are trapped by their dreams of former Empire and the vainglorious whims of individuals like Ambassador Mollari and the machiavellian Lord Refa. At first Londo thinks he can use his new friend Mr. Morden to further his own career, and is scarcely disturbed that the price is paid in Narn corpses. Disregarding all warnings, ("The Geometry of Shadows," "Knives") and the best chance for peace the Centauri have ever had, ("The Coming of Shadows") Londo oversaw the Centauri-Narn War from its inception as a border conflict ("Midnight on the Firing Line," "Chrysalis") to its culmination in the planetary bombardment of the Narn homeworld ("The Long, Twilight Struggle.") Yet as his dreams come closer to reality, his enjoyment of them ebbs, and it begins to dawn on him the extent to which it is he who is being used in the schemes of others.
The G'Kar who lied brazenly about the preemptive Narn strike against an undefended Centauri agricultural colony ("Midnight on the Firing Line,") is a far cry from the one who was ordered to petition Earth for sanctuary on Babylon 5 as the last surviving member of the Narn ruling body ("The Long Twilight Struggle.") In the intervening years he experienced a religious reaffirmation when he discovered on Z'ha'dum the ancient Enemy spoken of by the prophet G'Quon ("Revelations.") He learned futility by watching his warnings of the Enemy's return fall on seemingly deaf ears. And he learned humility from the greatness of his enemy's emperor ("The Coming of Shadows.") Perhaps these experiences have prepared him for the heavy responsibility he assumes of leading his people's struggle for independence in exile.
Signs from Earth have also grown markedly bleaker in just a few years. The anti-alien Home Guard ("The War Prayer,") the squelching of the Mars independence movement ("A Voice in the Wilderness,") and the increase in militarism back home ("GROPOS,") soon paled in comparison to the discovery of the conspiracy which led to the assassination of the Earth President ("Chrysalis," "Hunter Prey,") and the efforts of the insidious Ministry of Peace to eradicate the faintest whispers of dissent. In its most morally vacant act, the Earth government chose to sign a treaty of nonaggression with the expanding Centauri Empire ("The Fall of Night") rather than stand up for the sovereignty of the Nonaligned Worlds.
Whenever the Babylon 5 crew investigates the more disturbing situations arising from contact with Earth, they regularly find the Psi Corps lurking behind the scenes. Quite clearly the Psi Corps has no limits on the extent to which it will manipulate people in its efforts to obtain power ("Mind War," "Soul Mates," "A Race through Dark Places.") Among many who view them with suspicion, Commander Ivanova's hatred for the Corps is legendary; it is also a smoke screen to hide her fear that they will discover her telepathic latency. Within the Corps itself, there appears to be an even more dangerous, ultra-secret group operating under the code name Bureau 13 ("A Spider in the Web.") Among other acts of casual manipulation and destruction, they are likely responsible for planting the artificial personality in Talia Winters which was sent to spy on B5 and which wiped out Talia's true personality ("Divided Loyalties.")
Powerful, honorable, the Minbari almost annihilated Earth after their first encounter with humans, yet inexplicably surrendered in their hour of victory and subsequently helped sponsor the Babylon Project. Of the few humans and Minbari who know the complete story, many do not believe it. When the Grey Council war cruiser was poised over Earth during the Battle of the Line, a lone pilot attempting to ram their ship (Jeffrey Sinclair) was captured and interrogated ("And the Sky Full of Stars.") To their horror, the Council determined that Minbari souls were being reborn in human bodies. Besides the fact that Minbari refuse to harm their own, an ancient prophecy claimed that a great challenge would someday arise which could only be met when the two halves of the Minbari soul were joined. Thus, the Council ordered the Minbari forces to surrender ("Points of Departure.") Many Minbari, particularly among the warrior caste, still despise this decision ("There All Honor Lies,") and as the warrior caste grows more powerful on Minbar, there are signs of schisms appearing in the formerly coherent society.
The prophecy also mentions an individual who will lead the combined forces of Minbari and humans. So strong is her belief that she is this Chosen One ("Comes the Inquisitor,") that not only does Delenn refuse the Grey Council's selection of her to be the leader of all Minbari ("Babylon Squared,") but against its instruction to wait she metamorphoses into a human-Minbari hybrid ("Chrysalis," "Revelations.") Although permitted to remain as ambassador on B5, Delenn's confidence is severely shaken when the remaining Grey Council decides to remove her from their company ("All Alone in the Night,") and even further when she discovers that she is accepted by neither humans nor Minbari ("And Now for a Word," "There All Honor Lies.") She has only her faith in herself, the loyalty of Lennier and her growing bond with Captain Sheridan to depend on.
Delenn also appears to have the approval of the Vorlons -- although this is no easy burden. Enigmatic and extremely advanced, the Vorlons rarely seem to take the opinions of others into consideration when they act. They have visited many worlds, but not openly, perhaps to guide the species there, and perhaps to manipulate them. Kosh is willing to aid the few like Delenn and Sheridan who merit his attention ("There All Honor Lies," "Hunter Prey,") but they do not escape the encounter unscathed ("Comes the Inquisitor.") Since he arrived on the station, Kosh remained hidden inside his encounter suit for years. When he finally revealed himself, he appeared as a glorious being of light and lore -- different to each species who saw him. Very few realized that it was Kosh whom they saw, but most agree that they witnessed proof that the station is blessed ("The Fall of Night.")
After surreptitiously testing the attitudes of his crew for several months, Sheridan involved Ivanova, Garibaldi and Franklin in an extremely dangerous plot to investigate and root out the evil they see growing in the heart of the Earth government. At first they were all alone, with the exception of Sheridan's contact, General Hague. But as the Shadows come and darkness grows deeper throughout the galaxy, Babylon 5 has attracted unexpected allies for a great battle that looms heavily on the horizon. The first is Draal, who is the Minbari heart of the great machine and extremely powerful weaponry in the planet below the station. Assistance also comes from the embassy on Minbar, where former station commander Sinclair leads a growing army of mostly human and Minbari Rangers. In the vicinity of Babylon 5 the Rangers answer to Delenn and Captain Sheridan. Yet even with Draal and the Vorlons among them, by 2260 the fighters for the light seem pitifully few and weak compared to the pervasive and terrifying power of the Shadows.
"Matters of Honor" brought Marcus Cole, a Ranger, to the station; he led Sheridan and Delenn to a new ship, the White Star, a combination of Minbari and Vorlon technology. Pushing the White Star to its limits, Sheridan destroyed a Shadow cruiser. Londo attempted to sever his ties with the Shadows. Morden met with a Psi Cop, apparently far from the first such meeting.
The Centauri sent a replacement for G'Kar to the station in "A Day in the Strife" and threatened to persecute the families of G'Kar's supporters unless he gave up his exile and faced trial. Meanwhile, Ta'Lon, a Narn whose life Sheridan saved some months earlier ("All Alone in the Night") pledged to act as Sheridan's bodyguard. Londo arranged to have Vir sent off to Minbar as the new Centauri diplomatic liaison.