In my experience, the differentiator is the underlying emotion. Facts aren't as clear-cut as we like to think. You can't simply say you'll follow the facts; a certain amount of reasonableness is also required for combining those facts, which is a fuzzy and uncomfortable concept.
Conspiracy theories usually can't be disproven (almost nothing can, when you get down to it). They usually aren't completely fictional, lacking any shred of possible evidence. Their hallmark trait is the fact that they aren't driven by an even-handed search for truth, but by fear, anger, and paranoia. We like to think that truth-seeking is immune to these emotions, but it really isn't. Emotion keeps theories going even when they're wildly unreasonable, because they're still impossible to totally disprove.