- "And the Sky Full of Stars": The first true Wham Episode, that fills in the "hole in [Sinclair's] mind." It actually answers questions, replacing them with new questions.
- "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. It's Wham status takes a while to sink in, as repercussions from that episode start being felt later in the series. JMS stated that the title of the episode was meant to be a hint that it was more important than it looked at first glance.
- "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. Londo begins his Deal with the Devil as the Shadows annihilate a Narn outpost at Quadrant 37. And at the end...the assassination succeeds. The President is dead. As Sinclair puts it, "nothing's the same anymore."
- "The Coming of Shadows": This episode is the kind of thing JMS meant by a Wham Episode. It starts off looking like a light episode; the Centauri Emperor is coming to visit the station, and G'Kar's not happy about it. However, by the end of the episode, 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 .
- finale, "The Fall of Night": Earth's slide into fascism and a Government Conspiracy comes into the fore, Kosh's encounter suit opens and we see what's inside, and the Shadows become public.
- "Point of No Return/Severed Dreams": Earthgov cements its control over Earth media, the last bastion of freedom there. Babylon 5 secedes from the Earth Alliance, making a stand against the Clark regime.
- "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 FaceHeel 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.
- "Into the Fire": The Shadow War ends. Yes, it wasn't even a season finale — one of the major Myth Arcs ends on a random episode. Wham.
- "The Face of the Enemy": Garibaldi betrays Sheridan, leading to his capture. Also, turns out Bester has been doing far more behind the scenes than most people ever suspected.
- "Endgame"/"Rising Star": The end of the Earth Civil War. Sheridan is president of the newly-formed Interstellar Alliance, and Sheridan and Delenn marry.