This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "The Wheel of 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.
The Shadow War came to an abrupt end in "Into the Fire." Confronted by a united fleet of the younger races they were supposed to be shepherding, the Vorlons and Shadows attempted to force Sheridan to choose one of the two approaches to growth and evolution. Sheridan rejected both choices; the younger races didn't need shepherding any more, and would never again act as pawns. The Shadows and Vorlons, convinced that their battle for philosophical dominance could no longer continue, departed for the Rim, accompanied by Lorien and the last of the remaining First Ones. Londo, meanwhile, destroyed the Shadow base on Centauri Prime, earning a promise of retribution by the Shadows' allies.
Postwar euphoria was brief; with the departure of the Shadows, President Clark turned his attention back to Babylon 5, launching a propaganda war in lieu of a futile direct attack. In "Epiphanies," Sheridan was alerted to the first phase of the war by psi-cop Bester, who demanded to be taken to Z'ha'dum in exchange for the information. The crew arrived in time to see the Shadows' dark servants escaping with unknown quantities of Shadow technology, just before the sudden self-destruction of the entire planet. Their first target: Centauri Prime, where they planted a Keeper ("War Without End, part 2") on the body of the newly-appointed Regent. After receiving a mysterious coded message, Garibaldi resigned his post.
Delenn returned to Minbar to begin "Atonement" for her cross-species relationship with Sheridan, strictly forbidden by traditional Minbari beliefs about racial purity. Under the influence of a mind probe, the first days of her membership on the Grey Council came to light, including the fact that she ordered the start of the Earth-Minbari War. More importantly, she discovered that she was a direct descendant of Valen, and thus wasn't a racially pure Minbari to begin with -- and neither were untold millions of other Minbari descended from Sinclair's children of a thousand years ago.
Garibaldi, now operating as a private investigator, grew tired of the cult of personality surrounding Sheridan. In "Racing Mars," he agreed to help a group that claimed to be concerned about Sheridan's personality becoming a danger to the cause.
Tensions on Minbar continued to rise. In "Lines of Communication," the warrior caste began purging major cities of religious and worker caste members. In response, Delenn was asked to enlist the aid of the Drakh, one of the Shadow's servant races, now at large with looted Shadow technology. No bargain was struck.
Garibaldi was offered a job on Mars, and Sheridan devised a plan to deploy the White Star fleet as a police force to protect border areas from raiders and the Drakh, in "Conflicts of Interest." Garibaldi's new employer, a medical-research magnate, came into possession of a substance that allegedly cures a deadly genetic flaw in telepaths.
Delenn and a high-ranking warrior caste member, Neroon, tricked the warrior caste's leader into bringing the civil war to an end in "Moments of Transition," forming a new Grey Council under the majority control of the worker caste. Meanwhile, Bester struck a deal with Lyta, giving her the appearance of rejoining the Psi Corps. Earth forces attacked a convoy of unarmed refugee ships, causing Sheridan to declare war.
Sheridan's forces liberated the colony at Proxima 3 in "No Surrender, No Retreat." Disgusted with Sheridan's guns-blazing approach to unseating Clark, Garibaldi left the station to meet with his new employer on Mars.
Dr. Franklin benefited from "The Exercise of Vital Powers," in this case Lyta's ability to reawaken the frozen Shadow-implanted telepaths. Garibaldi arrived on Mars, where Mr. Edgars, his new employer, convinced him to try to lure Sheridan into a trap.
Garibaldi's trap was sprung, and Sheridan was captured by Clark's forces in "The Face of the Enemy." Edgars revealed his plan: to enslave telepaths by infecting them with a lethal virus. Unfortunately, Bester scanned Garibaldi -- who had all along been acting as Bester's agent, personality altered so he'd be more susceptible to betraying Sheridan -- and discovered the plot. Edgars was promptly murdered and the virus stolen.
Continuing the fight in Sheridan's absence, Ivanova was mortally wounded in "Between the Darkness and the Light." Shortly thereafter, Sheridan was rescued by Franklin, Lyta, and Garibaldi, who submitted to a scan by Lyta to prove he was manipulated by Bester. The League of Non-Aligned Worlds, at the urging of G'Kar and Londo, committed forces to aid Sheridan's fleet.
Using the implanted telepaths' ability to merge with computer systems, Sheridan's forces defeated the defenses of Mars and Earth with few casualties in "Endgame." Clark committed suicide rather than face capture. Marcus used the alien healing device ("The Quality of Mercy") to sacrifice himself to save Ivanova's life.