Board Thread:Legitimate Canon Questions/@comment-67.82.1.39-20140303011506/@comment-4091815-20140303033852

When Stiles, Allison and Scott "died" at the end of Season 3(a) to save their parents, they opened a door in their minds that let a little darkness in.

As we saw in the opening episodes of 3(b), they had side effects of that open door (hallucinations, waking dreams etc..). Deaton warned them all that they needed to close that door in their head or something really bad might use it to come in through the darkness.

This is, to our understanding, how the dark spirit of the Nogitsune got into Stiles head.

There is also what Derek said about Kira's Foxfire giving the Nogitsune a boost in getting control of Stiles, but we're not real sure how that part worked.

So -
 * Stiles Opens Door to Darkness in Brain
 * Nogitsune gets into Stiles Brain through Open Brain Door
 * Stiles Brain now Possessed by Nogitsune

I hope that's clear.