StarCraft II’s plot is trying as hard as it can to pretend Brood War never happened, short of actually making any retcons.
In Brood War, a new Terran faction is introduced, the United Earth Directorate, so powerful that they force all the other factions (including Zerg and Protoss) to band together to defeat them. They succeed in this, so it makes sense that the UED is no longer the overwhelming force they were in Brood War, but they’re a total non-entity in StarCraft II and Arcturus Mengsk’s Terran Dominion is again the dominant Terran faction in the sector, just like it was at the end of the core game.
In Brood War, Fenix is killed by Kerrigan during her second betrayal. In StarCraft II, they reverse this to make Fenix alive again, again. It’s not even the first time he came back to life, so it’s not like this is some unprecedented break in the lore (and Edmund Duke, killed in the same betrayal, gets to pound sand in Hell), it’s just the reversal of another one of Brood War’s plot points.
Most jarringly of all, in Brood War, Kerrigan fakes a face turn, falsely claiming her evil Queen of Blades persona was a result of the Overmind’s control and ended when it was killed at the end of the core game, and then it turns out nope, she’s still evil, and she betrays the rest of the anti-UED coalition twice in order to come out of the titular Brood War as not only the ruler of all Zerg, but also the dominant power in the sector. After her second betrayal, her pre-infestation lover Jim Raynor swears that he will be the one who kills her. In StarCraft II, Kerrigan’s evil Queen of Blades persona turns out to be the result of the dark influence of Amon, a secret turbo-Overmind who was controlling the Overmind. Jim Raynor finds an ancient alien artifact that reverses Kerrigan’s infestation and makes her a good guy again, so, exactly the opposite of the direction the narrative went with her in Brood War.
This is the main plot of the Terran campaign of StarCraft II (which was released as a standalone game). The scene at the end of SCII where Jim Raynor carries Kerrigan’s deinfested body out of the hive cluster feels like an AU from Brood War. Like, yeah, Kerrigan has that line to Jim Raynor in the original game’s Zerg 4 about how she’s with the Zerg now, and coming as it is nowhere near the end of the game, that’s clearly setting up another beat. The obvious way to play it is that she is not, in fact, with the Zerg now, or at least not permanently, but Brood War’s payoff to that setup is that she fakes not being Zerg but then actually is Zerg. And also Kerrigan then has to be immediately reinfested so she can be the protagonist of the Zerg campaign.
The closest thing to a plot point from Brood War actually coming up in SC2 is when characters from Brood War make what amounts to cameo appearances. UED vice admiral Stukov is in Heart of the Swarm, but he got himself infested in the meantime so he’s basically just another infested Terran for Kerrigan to bounce off of and may as well be an original character. Kerrigan and Stukov were enemies last time either of them checked, which they have to clear out of the way before Stukov can take up his new position as Kerrigan’s sidekick. Duran, also introduced in Brood War, was Kerrigan’s previous infested sidekick, but is retconned as secretly being a psychic demi-god relevant to the plot of SC2, which has nothing to do with anything he did in Brood War. Duran may as well have been replaced with an original character for all he resembled his depiction in Brood War, and Stukov gets stuck playing Duran’s role for some reason.
It really seems like, when Blizzard finally got around to making SC2, they found they really didn’t like the setting they’d left themselves with at the end of Brood War and wanted to reset to just the core game being canon, but Brood War was really well received so they couldn’t actually do that and settled for completely ignoring every plot development.
Also, the final mission of Wings of Liberty, the Terran campaign of SC2, was a huge letdown. It’s a defense mission while a space artifact charges up to instakill the entire Zerg hive cluster. The Zerg forces are generated pretty arbitrarily, not coming in distinct attack waves the way a player actually harvesting resources and producing units would have to, but instead sending mobs of units almost continuously. The cut scene at the end of Jim Raynor and his marines retrieving the deinfested Kerrigan from the hives not only feels like an AU, it feels really unearned, since all I did was flip the switch on the Zerg-Kill-o-Matic. StarCraft 1 was almost entirely made of missions that were just a knock-down drag-out fight with a huge enemy base, and while StarCraft II’s reliance on alternative objectives was initially a breath of fresh air, there wasn’t really a single destroy-the-base mission in all of Wings of Liberty. And the final mission would’ve been the perfect place for it, a siege crawl across the surface of Char to reach Kerrigan’s citadel. A cut scene of marines walking through the tunnels in the aftermath would’ve been really satisfying coming on the heels of having just spent two hours cracking that base open with a fleet of vikings and banshees screening a company of siege tanks.
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