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When dealing with the Primal Zerg, you have no difficulty communicating, despite thousands or millions of years apart. At first, this can be shrugged off as the Psychic Link, until we find out that they explicitly do not have any psychic abilities. The brilliance comes when you pay attention to the things they say: Consume, survive, change. Little else. You're only communicating with them on the most basic level, using concepts any zerg can understand. The Ancient One seems to be an exception, able to express complex ideas like the nature of the Dark Voice, but he is very old, and a unique specimen. The fact that Kerrigan is also a massively powerful telepath is likely also a factor, what they can't express in words she'll pick of from their thoughts.
Everything that happened with Stukov makes sense when you consider who was holding him captive all those years and their role in Wings of Liberty. For years Narud and the Moebius Foundation could experiment and examine the only person ever to be cured of being Infested, along with re-infesting him too to see if it was possible. All this time except for having the artifact itself, the Foundation and Narud had all they had all they needed to revive Amon, which is where Raynor and company ultimately come in...
Sarah Kerrigan, as a Queen of Blades who maintains her humanity, looks very subtly different from her previous incarnation. So much so that you have absolutely no problem believing that she has turned over a new leaf. Here's the hint why... look at her eyes. The tiny little twitches of facial expression that save her from the Uncanny Valley response make her more human. Now why can she do that? She's herself again! She is no longer influenced by the Dark Voice, who has no need for such petty things as human emotions. It also helps that in her new form, she does not have glowing eyes by default.
Everyone knows that Narud and Samir Duran are the same entity but Kerrigan never mentions that they used to work together for a wile, back in Broodwar with Duran being Kerrigans henchman, making it seem like they just met for the first time. But remember: Kerrigan's memory of her "queenbitch" days was full of holes so she really may not have remembered him.
When Kerrigan reaches the Hyperion's bridge in the early part of the campaign, she gets pissed when she realizes Raynor has been left behind. One may think she's overreacting to emphasize how much she cares about Raynor, but remember what happened to her on Tarsonis. She was captured by Zerg and infested because Mengsk abandoned her, and now Mengsk's son has done the exact same thing to Raynor.
A long time ago, Jim Raynor promised to kill the Queen of Blades. When he's rescued by a Zergified Sarah Kerrigan, he squibs the chance she freely gives him to put a bullet between her eyes. It seems odd, considering his oath to avenge his friend Fenix, and there's a perfectly reasonable explanation- he knows that she's supposed to save the universe. He can't kill her. There's another more interesting reason; he already has killed the being that killed his friend Fenix. The being in front of him is Sarah Kerrigan, not the Queen of Blades. She died on Char when he used the Xel'Naga device on her, and the Sarah we see in Heart of the Swarm is a Sarah Kerrigan who turned herself into a Zerg, not the unholy Queen of Blades that used her for its own purposes.
Kerrigan's trolling of Valerian during the first mission seemed like her having a sadistic sense of humor, but remember who she's dealing with; the last Mengsk who tried to control and use the Zerg destroyed a whole planet and was directly responsible for her becoming the Queen of Blades. Evil is not a Toy indeed. It also gives her approval of Valerian a lot more meaning compared to simply that he loves his people.
Donny Vermillion had a back and forth with Kate Lockwell about a possible Zerg-Human alliance because of the Queen of Blades's human side. Kate understandably tells him otherwise. In the final mission of Heart of the Swarm, it is because of Kerrigan's human side that called Raynor back to help her, forming a Zerg-Human Alliance.
The Dark Templar Saga series of novels makes a lot more sense now. With Wings of Liberty it seemed like the trilogy was just a cool side-story to introduce a few concepts important to the sequel. Now with the knowledge that Ulrezaj almost certainly worked for Amon, he and Zamara being sealed in a crystal kept on Shakuras, Valerian being friends with Jake and Rosemary, Zeratul being sent off to witness a bunch of energy creatures that we know from other novels absorb psionic energy. The trilogy is pretty much a novelized prequel to the sequel trilogy, its plot elements are weaved into the games much deeper than was apparent from just Wings of Liberty.
For that matter, a lot of the points that were first posited in the original starcraft make a lot more sense under the lens of starcraft 2. For example, why would the Overmind go through the effort of infesting Kerrigan using the best methods at its disposal and giving her free will when he is trying to assimilate the protoss to achieve perfection? To free the zerg of Amonís influence. Duranís reference to a far greater power that has slept for many millennia is elaborated upon by Kerrigan referring to Amon as Dead, for which the word sleep can allude to.
All of the Primal Zerg leaders are recognizably older, larger, more evolved versions of the regular Primal Zerg types - Brakk is an ultralisk, Slivan is a swarm host, et cetera. And Zurvan? Well, the first, oldest, most badass Primal Zerg ever to exist is, of course, the world's largest, angriest, most evolved Zergling.
With the revelation that Narud was in charge of the Tal'darim and the implication that he was Duran, the Excuse Plot of the Protoss missions in Wings of Liberty becomes more clear. As the campaign progresses and Jim finishes more of the Artifact missions, the crew of the Hyperion becomes weary of them, to the point that even Tychus starts having second thoughts about doing them, even going as far as calling the last one a suicide mission, the thing is, they are. Jim is regarded as one of the most cunning commanders in the StarCraft universe, to the point that even the Queen of Blades acknowledged it. Duran knew this as well, so, by making him fight with the Tal'darim, he was in a win-win situation: if Jim survived all of the Artifact missions, then, he could still use him to deinfest Kerrigan, use Tychus to kill her and still pose as Narud without problem; if he died, then he would no longer had to deal with him, he could still assemble the Artifact offscreen and the Dominion expedition to Char would have failed, leaving the Terrans with less defenses against the Zerg. This is somewhat reinforced by Word of God which states that there were various agents to get the job done, Tychus was simply the one that was the closest to accomplish the deed.
Towards the end of the game, Arcturus presents himself as a selfless leader and emphasizes his protection of humanity, even in private communications. Could be Alternate Character Interpretation. Or it could be that after the disaster in Media Blitz, Mengsk knows that anything he says, even in private, might come back to bite him.
Mengsk was in possession of the Xel'Naga artifact all along, which obviously raises the question of why he didn't used it to defend Augustgrad of the Zerg. Simple: he didn't care. For him it didn't matter if Valerian died, Warfield was killed or Korhal was overrun and many innocents died, all that mattered to him was that Kerrigan died.
The Hearts campaign was shorter and a fair bit easier than the one in Wings. Then, you remember the situation at the end of Brood Wars: Arcturus was granted Cruel Mercy by the Queen Bitch. The Hearts campaign was a reminder to the players just how easily the Dominion can be crushed by the Swarm. Kerrigan just has to give the order.
When the opening cinematic for Heart of the swarm was released, a lot of people were having fun with the viking landing to fight the ultralisk, and the zerg winning by attacking through choke points using lots of zerglings and ultralisks just seemed a Gameplay and Story Segregation for the cutscene. Cue the Korhal missions, where landed vikings are one of the more common enemies, the need to build a fast army leads to ultralisk based armies often, and it is common to attack over bridges and through streets.
In the end Kerrigan finishes off Arcturus for good, cursing him for having "turned us all into monsters". The "us" she is referring to is actually the entire Terran faction. Because of Mengsk's Dominion, the Terrans had been pushed into a villain role for all the games. Things may finally get better now.
As an expansion, in the ending cinematic of Heart, we see Kerrigan lifting off from the palace while Jim watches. The thing is, if you look closely, the debris of Mengsk's explosion is behind Jim, meaning that the Xel'Naga artifact is still in one piece in the intact part of the room.
Why were the Primal Zerg so against waking Zurvan? Because the pack leaders knew that as the strongest, they're the ones he's most likely to devour in hopes of evolving further.
The interaction between the Zerg Swarm and Primal Zerg mirror, to an extent, the original reactions of the Khalai Protoss to the Dark Templar in the first game. By becoming Primal, Kerrigan became the Zerg equivalent of Tassadar.
Maybe it has something to do with the fact that apparently there are no longer any living Xel'Naga in the universe.
When Stukov assists in the final mission, his entire army consists of aberrations and infested terrans of all kinds. This seemed like to just play to his type (Dehaka uses Primal Zerg while Zegara uses standard Zerg fare) until you realized that they probably still had the virophages on Skygeirr Station. Especially since the guy in charge of the defense noted how they should put the infected out of their misery, implying he saw it as a fate worse than death. Stukov is probably using this to get his revenge for being imprisoned for 4 years as a lab rat.
If you spoke to Ariel Hansen about the Artifact in Wings of Liberty, she notes how the Artifact is only a few thousand years old, as opposed to the millions of most Xel'Naga artifacts. It can de-infest infested Terrans, and cause severe damage to other zerg. It can also siphon energy from one being into another. Seems pretty convenient, that it just so happened to be able to destroy Kerrigan's control of the swarm and channel energy into Hybrids for Amon. But if Amon found out about the Overmind's plot to create an independent leader for the Swarm, the artifacts might have been created by Amon in the event of his death, as well as a failsafe in case Kerrigan was not completely under his control. It would explain why the Tal'Darim were guarding the pieces; they already knew why they are important and why they must not be stolen. They just had no idea Raynor was working for Narud at the time.
Dark Origins showed that Terrans somehow had access to Protoss Tech and genetic data for making Hybrids. Wings of Liberty showed the Dominion, who are not exactly on good terms with any protoss faction, having access to protoss genetic data. Granted, they could have been scavenging battlefields and possibly kidnapping protoss for this expressed purpose, but it would make more sense that Narud was manipulating the Tal'Darim to hand over "volunteers" for experimentation. Given their subsequent connection, this might be where all the protoss genetics came from for their Hybrids. Who the "volunteers" are is also pretty obvious: the Tal'Darim have been shown, on several occasions, kidnapping their Shakuras kin for no other explicit purpose.
A minor one, but given the Dominion's actions in the second mission, Arcturus Mengsk effectively declared war on the Umojan Protectorate. Who knows what kind of Terran vs. Terran war was occurring while Kerrigan was away on Zerus. It might also explain why Korhal is not more heavily defended by the time Kerrigan arrives.