This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "War Without End, Part Two." Note that this is chock full of spoilers!
"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.
In "Passing Through Gethsemane," Lyta Alexander, the station's first telepath and the person who unmasked Talia's Bureau-13-implanted personality, returned from a stay on the Vorlon homeworld to become Ambassador Kosh's attache. The Vorlons appear to have modified her, possibly even enabling her to carry one of them inside her.
The conspiracy of light made its move against President Clark in "Voices of Authority" by releasing a recording of Morden and Clark planning Santiago's assassination. Ivanova located another race of First Ones and secured a promise of help in the fight against the Shadows.
G'Kar learned of Londo's involvement with the Shadows in "Dust to Dust." He was sentenced to prison for assaulting Londo, and was visited in a dream by Kosh, who posed as the Narn deity G'Lan.
In "Point of No Return," President Clark declared martial law on Babylon 5 after dissolving the Senate back home. An attempt by the Nightwatch to take over the station was foiled, barely, but Sheridan was forced to accept G'Kar's help and begin using Narn as station security personnel.
Despite his temporary victory, Sheridan was soon forced to cut the station's ties with Earth in "Severed Dreams," following in the footsteps of several secessionist colony worlds after the bombing of civilians on Mars. Delenn, meanwhile, confronted the Grey Council about its unwillingness to intervene in the spreading Shadow-initiated conflicts among the nonaligned worlds; the confrontation led to the shattering of the Council. A losing battle for control of the station was resolved only by the arrival of Minbari cruisers under the command of Delenn and other former Council members, who declared Babylon 5 under Minbari protection.
In "Ceremonies of Light and Dark," Sheridan admitted his growing affection for Delenn. Londo threatened Refa with death unless the Centauri broke off their relationship with Morden and the Shadows.
Vir returned to the station after being demoted for running an underground railroad for Narn refugees in "Sic Transit Vir."
Realizing that the station would be better off with more protectors than just the Minbari, Sheridan and Ivanova negotiated with several minor races to supplement the station's defenses in "A Late Delivery From Avalon."
Bester delivered a "Ship of Tears" to the station: a Shadow-bound cargo ship with hundreds of cybernetically enhanced human telepaths. Telepaths, the crew soon discovered, can disrupt the link between Shadow ships and their pilots.
Franklin resigned his post as chief medical officer in "Interludes and Examinations." Morden tricked Londo into vowing to crush Refa, and asking for Morden's help to do it. Sheridan convinced Kosh to mount a Vorlon attack on a small Shadow fleet. The Vorlons won the battle, but in retaliation, the Shadows killed Kosh.
In "War Without End," Ambassador Sinclair received a personally addressed letter from 900 years in the past. The note brought him to Babylon 5, where he led Delenn, Sheridan, and others in an expedition to pull Babylon 4 a thousand years into the past, when history recorded its role in the defeat of the Shadows. Draal, in the Great Machine, opened a time rift, and sent his aide Zathras with time-travel equipment and the chrysalis machine Delenn would eventually use to become half-human. During the time shift, Sheridan was pulled forward seventeen years to find himself in Londo's throne room on a ruined Centauri Prime.