"Signs and Portents": Plays like a standalone for the most part, then in the last few minutes we get our first glimpse of the Shadows, and Sinclair sees a vision of the station being destroyed.
"Babylon Squared": The reason for Babylon 4's disappearance is revealed (it got Unstuck In Time). Visions of a not-too-distant future are seen, and it's not pretty. We learn of Sinclair's eventual destiny as The Chosen One.
The finale, "Chrysalis": Garibaldi discovers an assassination plot against the President, but is shot in the back—by his own right-hand man, survival uncertain. Delenn enters a cocoon, her future equally unclear. And at the end...the assassination succeeds. The President is dead. As Sinclair puts it, "nothing's the same anymore."
"The Coming of Shadows": Mollari's dealings with Morden reach a zenith, and the Centauri officially go to war with the Narn.
"In the Shadow of Z'ha'dum": Sheridan (and the viewer) learns who the Shadows are, and the role of Morden...and what happened to his wife Anna.
"The Long, Twilight Struggle": The Narn-Centauri War comes to a horrifying conclusion, with a Centauri fleet bombarding the Narn homeworld with weaponized asteroids, the Narns surrender and G'Kar is stripped of his position as ambassador and is given sanctuary
"Interludes and Examinations": Sheridan convinces Kosh to bring the Vorlon fleet to bear against the Shadows, which convinces the League of Non-Aligned Worlds that the Shadows can be stopped. However, in retribution (for breaking their rules of engagement), the Shadows kill Kosh.
"War Without End" (Two parter): Sinclair is back! It is revealed that Babylon 4 was stolen by the crew of Babylon 5 itself (!) for the purpose of bringing it back in time to assist in the first Shadow War one thousand years ago. Upon learning this, the crew does just that, after which they learn that The One spoken of by Zathras in Babylon Squared is actually three people (Sinclair, Delenn, and Sheridan, in that order). Sinclair then goes back in time with Babylon 4, uses the transformation ritual used by Delenn at the end of season 1, and turns into a Minbari (the prophet Valen, to be exact).
Season 3 finale, "Z'ha'dum": Sheridan's wife is Not Quite Dead after all, but has undergone a Face Heel Turn; we learn the Shadows' agenda, and they suffer a crippling blow. However, as Kosh had predicted, Sheridan is apparently dead, and Garibaldi is missing.
Season 4 is actually so full of major universe-affecting events that it could be argued it's one huge Wham Episode.
"Into the Fire": The Shadow War ends. Yes, it wasn't even a season finale — one of the major mytharcs ends on a random episode. Wham.
"Endgame"/"Rising Star": The end of the Earth Civil War. Sheridan is president of the newly-formed Interstellar Alliance, and Sheridan and Delenn marry.