Since Kerrigan and Raynor sort of had something going on in SC1, now that Kerrigan is "human" like again and Raynor is obviously, for some reason, still in love with her, I think it's plausible that Kerrigan's human emotions would revitalize and regain feelings for Raynor. However due to the swarm and the wars going on, it's hard to keep a relationship right? So Kerrigan sends a special zerg spy to watch Raynor and make sure he's still alive and see what he's up to (like an invisible protector).
That's when the missions kick in. We play Raynor's Terran and, while we play through the story of HOTS, we see what happens to Raynor in a more first/third person kind of way. This could allow us to keep up with the terran's role in everything in a realistic way.