This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "Soul Mates." Note that this is chock full of spoilers!
In "The Geometry of Shadows," Refa, a high-ranking Centauri noble, asked Londo to pledge his help in seizing the throne at some point.
In "A Distant Star," Lt. Keffer saw a Shadow ship in hyperspace and vowed to find out what it was.
"A Spider in the Web" revealed a mysterious "Bureau 13" operating out of the San Diego wastelands. An assassin, controlled by the Bureau, attempted to thwart a peaceful settlement of the situation on Mars. Scanning his mind, Talia saw a Psi Cop present at the operation that programmed the assassin, but she didn't tell anybody else. Sheridan's interest in conspiracy theories was revealed as he attempted to solve the puzzle, and the existence of a plant among the B5 crew, code-named Control, was hinted at.