This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "Infection." Note that this is chock full of spoilers!
The pilot, "The Gathering," was set in the year 2257; Babylon 5 had recently come online. The last of the ambassadors, Kosh, arrived on the station, prompting an assassination attempt. Sinclair was framed for the attempt, but was eventually cleared when the real culprit -- a Minbari -- was discovered. Many mysteries were introduced: Sinclair's missing 24 hours on the Battle of the Line (with the announcement by the Minbari that "there is a hole in your mind"); the mystery of Kosh, seen only by the doctor and the telepath; and the disappearance or destruction of the previous four Babylon stations.
Season One began with "Midnight on the Firing Line," about 6 months later. Lt. Cmdr Susan Ivanova replaced Lt. Cmdr. Takashima as second-in-command; her dislike of the Psi Corps became evident when Talia Winters arrived. A Centauri agricultural outpost was attacked without provocation by the Narns. (In broad strokes, this episode portrayed the Narns as the "bad guys" and the Centauri as comic relief.) Luis Santiago was reelected President of the Earth Alliance.
A "Soul Hunter," a member of an order which collects and preserves important souls, found himself on the station, and attempted to collect Delenn's soul prematurely. The Minbari, it was revealed, greatly value souls; they prevented a soul hunter from taking the soul of their great leader Dukhat, so that his soul would be reborn into the next generation. Delenn was called Satai by the soul hunter, which prompted Sinclair to wonder if something was going on, as Satai is the title used my members of the Grey Council, the Minbari ruling body and highest religious authority.