Allison is killed in some battle for Beacon Hills (or is presumed dead, author’s choice). Chris and Isaac come together in their shared grief, because the other is the only piece of Allison they both have left. And at first it’s just a way to stop thinking about the hole in their lives, to not hurt quite so much just for a little while. Chris (or Isaac, if he’s your pov character) doesn’t know when it became something more.
(No, I don’t want Allison to die, and no I don’t advocate the idea of killing a female character merely to give the male characters more man-pain, but this idea came to me after
reading meta regarding the comments that have been made (by Jeff Davis and others) suggesting that one of the five main characters (as shown in the title sequence) is going to be killed off this season.)