Ow, My Sanity/WMG

The end of the storyline will involve the creation of a Half-Human Hybrid
You have two young people forming a relationship under very unusual and treacherous circumstances. Furthermore, the Black Goat of the Woods with a Thousand Young (aka Shubby) is acting as the Dyer House den-mother, a mask of the Crawling Chaos is in close contact, and a Shoggoth Lord masquerading as a child, is living among them. The fact that the Sleeper of N'kai offered this to David shows that it is quite doable. It's either going to be her or Nancy with our young Mr. Bartlett that creates said offspring.
 * It being doable is supported by a few things in the Mythos (eg, Wilber Whateley and other Fosterlings of the Old Ones), although in this case the genders are reversed from how things normally go, not to mention most likely being more, er, direct, in how it's accomplished.

Theories about what the Deltas suspect David of being
Come on, I know you've got them. Let's hear them.


 * A mask (implied by a comment of the author over on Deviant Art).
 * A full-blown Eldritch Abomination

At some point time travel is going to be involved
It's as good an explaination of why there's an ancient Egyptian tablet showing David telling off Set (who may or may not have been Nyarly) as any, particuarly since it's more or less supported by Word of God.

When the comic ends, David won't be human anymore
The author has stated that there's going to be a Lovecraftian ending, of which there are three varieties; main character dies, main character goes mental, and main character becomes something else. Given that option three is both the most interesting and the most in keeping with the comic so far, this troper predicts that it'd going to happen. Strangely, given David's life so far, it could still qualify as a happy ending, for him at least.
 * Or maybe he wasn't human from the start.
 * Maybe he will be the sprite... fairy... thing that gave the dagger to the Hyberborean wizard, having traveled back in time with it so it could perform its important roles.

Delta Green will eventually ally with the Dyer housemates against something worse

 * Such as? I mean, I know that the Lovecraft-verse has some seriously scary stuff but most of the Dyer house residents are pretty damn high up in the scary crap hierachy.
 * Perhaps a tentative peace then? As long as no one else is eaten or gets wind of the weird, no more attacks?

If/when Nancy discovers 'nookie' neither she nor David will be seen for a few days
Based on what happened with the pancakes, Nancy has some definite Sense Freak tendencies, not to mention being new to the entire concept of 'liking' something. Some things are just inevitable.
 * Connects to some degree to the first WMG on this page, and this troper would not be surprised if the other girls run a betting pool on when the erstwhile couple will emerge.

David's parents originally came from Dunwich
Going by some comments of the author regarding certain future assumptions of David's parents regarding Shogga, I think it's safe to say that they're a special kind of stupid. Said variety of stupid seems to be endemic to Dunwich, at least it was back in the 1920's.