Last part of Starcraft:Broodwar

Episode VI: Chapter 8, To slay the Beast

Kerrigan kidnapped the Dark Templar Matriarch, Raszagal from Talematros and infested her. Zeratul and his forces ran after her. Kerrigan revealed to him that she kidnapped Raszagal so she could force Zeratul to kill the Zerg Overmind, since Dark Templar are the only creatures powerful enough to really destroy it. If he succeeds, Kerrigan would give back Raszagal. Raszagal convinced Zeratul to cooperate, saying that the demise of the Overmind was not for her nor for Kerrigan but for their people. Zeratul's Dark Templar cooperated in the mission. At the end, Zeratul and his Dark Templar succeeded and Kerrigan gave back Raszagal. But under Kerrigan's influence, Razsagal wanted to stay behind. Zeratul immediately found out that Kerrigan infested her.

Episode VI: Chapter 9, The Reckoning

Samir Duran reported to the Queen of Blades, Sarah Kerrigan that Zeratul had successfully destroyed the Overmind. With all of the Zerg Cerebrates (excluding the player, of course) and the Overmind destroyed, the whole Zerg reverted to Kerrigan's direct control. But there was one more problem to take care of. Zeratul managed to bypass Duran's defenses and "stole" back Raszagal. She was now being held captive in a Stasis Cell on Char. Zeratul and his Protoss forces were preparing to debark for Shakuras in thirty minutes. But Kerrigan's forces came and ruined his Protoss base. Kerrigan's Zerg forces destroyed Raszagal's Stasis Cell. Zeratul was forced to kill his Matriarch Raszagal because he didn't want her to live as Kerrigan's slave. After all that, Kerrigan allowed Zeratul to leave, thinking that he will never forgive himself for killing his own matriarch, a much better revenge than anything she had ever dreamed of.

Episode VI: Chapter 10, Omega

The infamous Queen of Blades, Sarah Kerrigan deceived and manipulated every leader of the different races and factions in the whole universe. She and her Zerg were involved in the deaths of a number of Protoss and Terran leaders; including General Edmund Duke of the Terran Dominion and Fenix of the Protoss. Her evil scheme forced Zeratul to kill the Dark Templar Matriarch, Raszagal. And Infested Duran assassinated the United Earth Directorates' (UED) Admiral Alexie Stukov. And above all, she and her Zerg destroyed, not only the lives of so many Terrans and Protoss, but including the lives of a lot of Zerg too. She made herself the enemy of all the other races.

Because of her heinous actions, the United Earth Directorate (led by Admiral DuGalle), the Terran Dominion (led by Arcturus Mengks) and the remaining Protoss survivors (led by Artanis) joined forces to destroy Kerrigan and the Zerg once and for all.

Apparently, the Queen of Blades was immune to karma. In the end, she and her frenzied Zerg forces obliterated the three forces in a single epic battle; thus claiming her title as "The Queen Bitch of the Universe"

The three admitted defeat, but gave Kerrigan and her Zerg an ultimatum that they will come back in the near future to destroy her and the Zerg.

Prior to this battle, Samir Duran mysteriously vanished and somehow, his psionic link to Kerrigan disabled, hindering Kerrigan from locating him.

"Ascension"

"Once again I stand atop the broken bodies of my enemies… Victorious but not unscarred. The Earth-borne Directorate has been destroyed, and the Overmind lies dead and trampled beneath the ashes of Char. As for my unlikely allies, I think that I shall allow them a reprieve, for in time, I will seek to test their resolve and their strengths. They will all be mine in the end, for I am the Queen of Blades. None shall ever dispute my rule… again."

- Infested Kerrigan in the last of Episode VI

"Dark Origins"

(If some of you are not aware, this is a secret mission. It plays a very crucial role in the Starcraft storyline. This can be accessed when you accomplish Mission 9 [The Reckoning of Episode VI in less than 25 min. This happened before "Omega")

Zeratul was searching for Artanis and his forces in Shakuras. He felt that a nearby moon was emitting psionic energies so he fled there to check it out in hopes of finding Artanis and his Protoss forces, but instead found something much more interesting…

Samir Duran mysteriously vanished. Kerrigan was not able to find him since his psionic link to her was somehow disabled. But she didn't care. She had to destroy the three fleets who challenged her.

This mission reveals the true allegiance of Duran. He was covertly doing an experiment on creating Zerg-Protoss hybrids which he kept inside Stasis Cells.

Zeratul arrived and was dumbfounded when he saw what's inside the Stasis Cells. He observed the creature inside the cell. All of a sudden, Duran's voice was heard. He said that he was doing this under the command of a "far greater power" that has slept for countless ages. He also said that he himself is a thousand millennia old and that he has been know by many names in the past. He added that the "far greater power" he serves reflects the creature within the cell.

Zeratul said that this is utter madness and that Duran doesn't realize what monstrosity he has created. Zeratul attempted to destroy Duran's experiment, but Duran said, in a completely inhuman voice, that destroying the stasis cell will not hinder the project because he has "seeded" the hybrid on multiple worlds. Zeratul won't be able to destroy them all before it's too late.

Many fans formed theories about "Dark Origin". A lot of people say that Duran was working for the Xel'Naga. They say that the ancient race wasn't extinct after all. Duran may even be a Xel'Naga himself! It is interesting to note that the Xel'Naga preferred to work covertly.

Other possibilities include that Duran is either working for the Overmind (since the Overmind had an ambition of assimilating the Protoss with the Zerg to make the Zerg perfect), or Duran himself was the Overmind or Duran had become Doran Routhe in some way.

Another theory opposes the first theory. It claims that the "far greater power" Duran serves is not the Xel'Naga, but another unidentified race, which is more powerful, considering that it possessed both purity of form and of essence and Duran claimed that his masters reflect the creature inside the cell. The Xel'Naga didn't have those, that's why they were striving to create such a race.

Another interpretation of the "reflection" is that the souls of the Xel'Naga somehow survived and are going to reincarnate in the hybrid.

This mystery is yet to be unveiled since Blizzard Entertainment cancelled the release of StarCraft: Ghost.

Reference: Wikipedia