So wait, Daniel is in Iraq? Just kidding. How lame.
Anyway, so I guess there are four options...
1. Daniel is passed out somewhere (hopefully with a girl!)
2. Daniel left Bree because he is sick of her attitude.
3. Daniel has been taken by Tachyon for some purpose.
4. Daniel has been taken by the Order.
Or...what if Daniel has been part of the Order all along? We now know that the Order has had a vested interest in Bree for quite awhile. So what if Daniel was a plant by the Order? After all, he has Bree's only friend from high school. And what if he has conflicting feelings? He knows what he is supposed to do because of the order but he cares for her too? Maybe all the research he did was just fake....after all, nothing has come from the photos found on Lucy's computer. And it would explain why they killed Mr. Bree but didn't take Bree. Because they know she is with Daniel and they are holding her there for some reason. We all know the Order can find her. They have found her easily enough before. I think Daniel pretended to be drunk to let Random Girl into the house for some reason. Random Girl is part of the order too and she has planted something in Jonas' house. So then the order tries to set up a romantic thing between Daniel and Bree to gain further advantage. It doesn't exactly work right..but it does have some effect because Bree is bothered by what Daniel is doing while he is missing. My guess is Daniel will be used to lure her someplace and when she finds out that everyone she loves is now gone..Dad dead..Mom with the Order, Daniel with the Order then she will give up and accept her fate. (But then something will happen so the story can keep going)
Ok wow..that was long and probably all wrong but that is my theory

Cassie was watching me.
Now I'm just lonely.