- The show takes its first drastic turn with the second season finale "The Jem'Hadar". While previous episodes are either self-contained or part of a brief or occasionally-visited Story Arc, this episode introduces a new antagonist, blows up a Galaxy-class starship (just like the Enterprise-D) and kicks off a Story Arc which grows increasingly important over the rest of the series.
- And the Wham quotient is only amplified with the season three opener "The Search Part I", which ends on a cliffhanger with Sisko, Dax, O'Brien, and Bashir's seeming death or capture, the brand new Defiant seemingly destroyed, and Odo finally meeting his people.
- Which is followed by "The Search Part II", in which it is revealed that Odo's people are the rulers of the Dominion.
- A particularly notable example is the 2-part episode "Improbable Cause"/"The Die Is Cast", with a "Holy Shit!" Quotient that's off the charts: Garak blew up his own shop, Tain is working with the Romulans to destroy the Founders, Garak is willing to forget that Tain tried to kill him and rejoin the Obsidian Order, Tain orders Garak to torture Odo and he DOES, Odo admits he wants to rejoin the Founders, Garak then protects Odo's secret and lies to Tain's face about it, the leader of the Tal Shiar is actually a Founder and the entire plot was a means to eliminate both the Obsidian Order and the Tal Shiar in one fell swoop... and the Founders' plan succeeds... whew.
- Season 4's "The Way of the Warrior" two-parter brings Worf onto the station and sees the Federation/Klingon alliance come to an end.
- Season 5's "In Purgatory's Shadow"/"By Inferno's Light" two-parter, which acts as something of a follow-up to the Season 3 arc. Tain is alive, is being held captive in a Dominion prison and is revealed to be Garak's father. Oh, and one of Tain's cellmates turns out to be Bashir, who was replaced by a Changeling weeks earlier. Not only that, but Cardassia joins the Dominion - giving them a foothold in the Alpha Quadrant. The Federation and the Klingon Empire reinstate their peace treaty to defend against the new threat.
- This is followed by "Dr. Bashir, I Presume" which is a wham episode for the good doctor. The revelation that he was genetically enhanced as a child and has been hiding it all these years pretty much rewrites his entire character, explaining a lot about what we've seen so far and having major ramifications for his future character arcs.
- "Call to Arms" - The Season 5 finale: the Dominion attack Deep Space Nine... and take it, returning Dukat to command; the Wormhole is mined, cutting off access to the Gamma quadrant; and Jake Sisko stays behind on the Dominion-occupied station.
- "Inquisition". Section 31. The fact that The Federation has its own equivalent of the Tal Shiar or the Obsidian Order that's been operating in secret for the past 200 years.
- Jadzia's death. While it was pretty much well known among fans that the actress was leaving the show and they were killing the character off, the brutality of an outright on-screen murder of a main character while praying at a temple altar was jarring.
- The manner of her death is also quite jarring: Dukat suddenly appears behind her and, using the power of a Pah-wraith, fatally wounds her on the spot, not completely unlike Tasha Yar's death in Star Trek: The Next Generation. It is this moment that solidifies Dukat going from a mere overzealous Cardassian soldier to a galactic threat!
- The A-Plot of the episode has the allied Federation, Klingon, and Romulan fleets launching an offensive into Cardassian space, conquering the Chin'Toka system despite heavy casualties. For over a year they had been struggling to defend themselves from the Dominion, but now the tide of the war has officially shifted in their favor.
- To top it off, Sisko, sorrowful over Jadzia's death and his failures as both the Emissary and a Starfleet officer, takes his leave of Deep Space Nine, taking his baseball with him; a gesture that suggests he may not ever come back...
- "Strange Bedfellows": The Breen join the Dominion. "The Changing Face of Evil": They attack Earth. And then they destroy the Defiant, and hundreds of other Alliance ships. This is why even the Klingons fear the Breen.
- And while that's happening, Damar launches his rebellion against the Dominion. The dynamics of the war have completely changed.
Wham Episode / Star Trek: Deep Space Nine