This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "Into the Fire." Note that this is chock full of spoilers!
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.
The alien, Lorien, claimed to be the first of the First Ones, the reason the Shadows always return to Z'ha'dum. G'Kar never found out "Whatever Happened to Mr. Garibaldi," and was captured by the Centauri. Londo promised G'Kar the freedom of the Narn homeworld if G'Kar would help him unseat Emperor Cartagia. Meanwhile, back on Babylon 5, the League of Non-aligned Worlds splintered thanks to Sheridan's disappearance, and Delenn summoned the Rangers to organize a final strike on Z'ha'dum.
Garibaldi was recovered from a mysterious ship in "The Summoning," while Ivanova and Marcus set out in search of more First Ones. What they found instead was a vast Vorlon fleet on a mission to destroy any world touched by the Shadows. Lyta turned against Kosh. Sheridan returned with Lorien, just in time to thwart an attempt by the frightened Non-Aligned Worlds to break up the Army of Light.
In "Falling Toward Apotheosis," Londo learned of Cartagia's plan to allow the Vorlons to destroy Centauri Prime, thus propelling him to godhood in a glorious explosion of fire. Londo convinced Cartagia to first go to Narn and try G'Kar for crimes against the Centauri; even so, Cartagia had a guard pluck out G'Kar's left eye in a moment of pique. As the Vorlon fleet proceeded with its plan, destroying world after world and sending refugees streaming to Babylon 5, Sheridan and Lorien battled and killed Kosh. Delenn learned that Sheridan's resurrection is only temporary; he has no more than twenty years left.
During "The Long Night" before the Army of Light's planned confrontation with the Vorlons, the Shadows unleashed their own planet-killer, prompting Sheridan to lure them into direct battle with the Vorlons to settle the conflict once and for all. With G'Kar's help, Londo and Vir assassinated Cartagia; the royal court, most unaware of the plot, elected Londo prime minister to quickly rid Centauri Prime of Shadow influence and stave off the impending Vorlon attack. Londo ordered the withdrawal of Centauri forces from Narn.