re: So who picked up Starcraft 2: Heart of the Swarm today?

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The book Flashpoint explains the gap. They are literally on the run from Mengsk the entire time. Over the course of the book, Narud (Duran from Brood War) reveals that he had been working for Mengsk the entire time, but Valerian turns on his father and smuggles Kerrigan out. Then the Raiders take refuge at Deadman's Point with Mira coming to their aid.

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Valerian Mengsk's Dominion fleet and Raynor's Raiders invade Char. After long and bloody combat, the xel'naga artifact is successfully activated, de-infesting Kerrigan.[23]

Arcturus Mengsk and the rest of the Dominion Armada arrive, intending to terminate Kerrigan. Valerian and Raynor flee with her, sparking a small scale civil war. Due to her illness, they meet up with Dr. Emil Narud, head of the Möebius Foundation to try to treat her. However, Narud betrays them and makes common cause with Emperor Mengsk. He escapes with the artifact, while Raynor and Valerian escapes, taking Kerrigan to a secret Umojan Protectorate laboratory.[24]

For over two weeks, Valerian subjects Kerrigan to a number of tests, seeing how she reacts to stimuli.[25]

Three weeks after the Battle of Char,[26] Dominion forces track down the Raiders and Kerrigan. Raynor is captured and Kerrigan is seperated from the Raiders. With nothing left save vengeance, she starts reforming the Swarm to achieve vengeance against Mengsk.

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