Supernatural Fanfic - Dean/John, Dean/Sam..
John expected his eldest son to present as an Alpha, like himself, but when Dean turns out to be an Omega, there's more than just disappointment in John's eyes. Medication can take care of it, though, damp Dean's scent, mute his Omega instincts; and his heats...well, John can take care of those, too.

Sam hates listening from the room next door to what John is doing to his beloved older brother, and when Sam finally presents as the coveted Alpha, he fully intends to do something about it.

But are Sam's plans the best thing for Dean? Is there something John hasn't told them? Something deadly? And will they find out soon enough that there are reasons for everything their father does.
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http://archiveofourown.org/works/3995092?view_full_work=true