Once Kerrigan takes Char back and becomes a Zerg, Mengsk reveals to her that Raynor is alive, but Kerrigan can't sense him. Still, she won't rest before she rescues Raynor from their grip, no matter what Raynor will do or say next. Mengsk, the man she hates more than anything, aptly adds that Raynor of all people would probably like to kill her now. But in her passion, does Kerrigan stockpile this as another reason to seek revenge on Mengsk? Does she simply ignore the gun that Mengsk is holding on Raynor and attack Mengsk regardless? No. Because once more, the hate is subsiding, and she begins to focus on something that pulls at her and speaks to her humanity - her love for James Raynor.
Now, this is where the few points of non-linearity kick in. For sake of argument let's consider SkyGeirr to be done before the rescue missions, although I personally rescued Jim first since I felt it would be a more in-character decision. At SkyGeirr the overarching "large conflict", not necessarily the central conflict, of Starcraft 2 is present, that of Amon and the Hybrid. Back on Zerus, the Ancient one Zurvan exposited to Kerrigan, and Zeratul warned her, that Amon would be returning and she'd need the power of Zerg to defeat him. But that was not at the time her concern - she survived the transformation fueled by what drove her to do it, the hatred for Mengsk and her need for revenge. She assaulted SkyGeirr to destroy the Hybrid, but she did not believe in the return of Amon... untill she had to face of with Narud personally.
The Shang Tsung fight with Narud is partially confusing. I entertain the idea that, well, what if Kerrigan believed that Raynor was some shape-shifting manipulator the whole time? That would seriously break her, or at least as was shown, give her pause. But her faith in Jim lets her see through the overdetailed disguise (seriously, cigarrete box, too?) and she begins assaulting Narud. But then he shifts into Kerrigan's old ghost form.
Now this is one of the points of confusion. It doesn't symbolise her inner conflict, because it's obviously just a trick. Does it symbolise her wanting a better life? Once again, just a trick. Was Narud planning to kill Kerrigan and then free Raynor and pretend to be deinfested Kerrigan? Well, that would be awkward. I think this one design choice is more than anything done for the trailer. There IS inner conflict in Kerrigan's character, but this isn't one of them.
Sure, I could cite "symbolism" but it would be very stupid to do so. However, the scene does serve it's purpose, since it integrates the overarching antagonist back into the plot without conflicting too much with the central theme, which was a small issue in WoL where the prophecy by its very existence could be said to challenge the theme rather than strenghten it.
Now, at this point is where I return to "Believe in me". Kerrigan has lost her identity at this point as she "became the Swarm" and more often than ever claims that she's the one responsible for Queen of Blades' actions before she rescues Jim. That is why when she does break into his cell and Raynor confronts her with the crimes she thought she commited, she hands him a gun and aims it at her head - her wish that if the only person who had really considered her good, the man who she loves, considers her the monster that she now also identifies as, then it is the truth, and she must die - vengeance or no, it won't matter. Her love for Raynor is more important. And Raynor, of course, doesn't fire, because he still knows that it is Sarah Kerrigan before him, and not the wretched Queen of Blades. But he knows something else - that Kerrigan's hatred for Mengsk was so fierce that she went through all the steps to reverse his actions to bring her back. Did she really love him more than she hated Mengsk? Of course not. So Jim did the right thing, and shut her down - "We're done." There's no way to sustain a relationship of romance when one of the parties is obsessed over another individual to the point of undermining all the efforts of the other party to sustain the relationship. Kerrigan returns to the leviathan now, more alone than she'd ever been before, and proceeds with what she had started out to do.
The invasion of Korhal takes ample opportunity to showcase that her humanity is largely returning and that she's not influenced by the Swarm's ruthlessness, rather instead forcing the Zerg to avoid slaughtering the populations and allowing for evacuation. Throughout the whole invasion, the Dominion is so well-prepared for the onslaught that at several times it actually seems like the Zerg are having more trouble taking Korhal than the Dominion did in taking Char. People may argue that the Dominion isn't supposed to stand a chance in this engagement, but I cite balance and say that the tensions would just not be strong enough if after all that's happened we'd know beforehand who will be succesful - and Mengsks confidence is so effectively bolstering the tension, since even towards the end the man never seems to feel defeated. And of course, there's the recknoning.
It goes without saying that the campaign had a lot of heartfelt moments available for all those that weren't just trying to run away from the story because "it's too soapy". But the return of Jim Raynor to fight with Kerrigan and the Reckoning was not only hearfelt, it was awesome. Raynor once again shows just how much of a greatest friend he is in always being there to back up the people he cares about to fight causes he believes in, while Kerrigan thanks him for his return to which he responds "Thank me later", which of course she does. Ascension is covered in "the ending is a masterpiece" thread, go ahead and check it out after you're done reading this.http://eu.battle.net/sc2/en/forum/topic/6893511212
Basically, after all the hatred has been vindicated, after Mengsk is finally defeated and killed, the hatred subsides. But she cannot return to Jim. She has a duty now, a career as the leader of the Swarm and must opposed the return of the fallen one. Even in the conflict of hatred and love, though love always must win through, sometimes happiness doesn't. Her purpose must come first, and she ascends back into the Swarm, thanking Jim, and after the last speech by Kerrigan the credits roll.
There's a very relavant theme here, and as I exposited, every plot turn and almost every aspect element contributes to it in one way or another. This is such a step up from Brood War, which carried itself on despair and shocking plot premises that got the characters killed, that it stands solid as the best Blizzard have done so far. SC1 carried itself on succesful and intricate plot and characters - Brood War ruined those, and SC2 has since resurrected them AND added what was missing for a real valid story, without the hollowness of being just another conflict plot - THEME.
After 3 years of dispute and controversy, after 5 months of debate and stalemates on plot contradictions and faulty writing criticism with both sides... after all the discussion that went nowhere on atmosphere and characters, after all the subjective interpretations, it is finally possible to say, completely objectively, which story arc is better, on this single element, this vital core of storytelling, that differentiates the two.
For all of these reasons, with respect to both Wings of Liberty and Heart of the Swarm, the Starcraft 2 trilogy has in so far proven a far superior story than SC1 or Brood War, and House Pro-SC2 FINALLY takes home the debate.