I did the campaign and I missed some information but looking at the prophecy, the hybrid take control of the zerg and kill the human and the protoss. Only kerrigan can stop them. Maybe she can stop them because she's an hybrid too and they cannot control the zerg while she is doing that. Now that she is de-infested the hybrid will have free space to control the zerg. I don't know what you think of it but I think it seem bad.
MASSSSSIVVE SPOILER ALERT DON'T READ THE POST ABOVE ME AND MOVE THIS TO SPOILER SECTION Spoiler Well they leave it open to why Kerrigan can save them or if Kerrigan even lost all of her powers. Kerrigan isn't a toss/zerg hybrid though and there are other infested terran out there. Perhaps its something Kerrigan knows or its her connection to the overmind, or its her psychonic powers or if the toss can do some fancy thing to her they can unite with the zerg or true loves first kiss with raynor will form some massive pulse which incinerates the Xel'naga?
Spoiler Or, you know, she might be re-infested during Heart of the Swarm in order to save the universe. Sure it's not a very original idea, but it's plausible.
Who says Kerrigan needs to be Zerg to stop the Xel Naga? Who says she has to be Zerg to still be the Queen of Blades Edit: I'm glad WOL ended the way it did. I'm sick of Blizzard letting the bad guys win and having horribly depressing story arcs. So I didn't think it was bad end at all. It was everything I was hoping for.
I've been waiting 10 years for Jim Raynor to get his girl back, and he finally did. It was very satisfying