From the first episode we know that Niki's alter ego is triggered when her life is in some sort of danger. It's also seen in 1.04 that her other personality comes out to play when her life and the life of her son is being threatened as well. So that's enough evidence to say that her "other half" looks out for her in some form or another. But I have a feeling that there's more to her alterself than what we've seen.
For instance, after another repeated blackout and traveling with Micah to their grandmother's house, Niki first has to bury the bodies at a specific location where her other personality wrote the directions of. When she arrives there, she finds a shovel at the spot and starts digging, assuming this the place in the middle of the desert would be safe (of course after watching CSI, this is false under any circumstance). But as she starts digging a hole big enough for all the dismembered body parts, she finds yet another dead and rotting body. Niki also finds a skull ring, which she later brings forth to the attention of the mother of her criminal husband, claiming that the ring was evidence that he killed whomever the ring belonged to. But even though Niki is convinced that her husband is a murderer and criminal, and potentially following them, Micah is also convinced that he didn't do anything wrong.
I'm thinking that her alter personality, while with good intentions of keeping Niki and her family safe from threatening situations, is actually the murderer of all those people. Perhaps framed her husband. It makes sense if she led Niki to that place, knowing all too well that she would find the ring, that perhaps there's a connection between the alter personality and other murders other than what we know of. Also, I have a theory that with her husband having the mysterious gift of snapping in and out without anyone knowing, that within the next episode he may want to take Micah away because he fears for his safety --- just like Niki fears about what might happen if Micah is taken with her acclaimed-criminal husband. But really, are both Niki and her husband enemies, or are they the same and just aren't aware of it? Or is Niki truly a threat to herself?
I have a feeling that Micah knows the answer, since not only is he a boy genius but he seems to understand and comprehend more than he's letting on. Perhaps the confusion between Niki and her husband can be cleared up by Micah and his perception, or whatever power he possesses.