All Nephilim have wings and secondary genders. And in a world where alphas and omegas exist, in a world where Alec is an alpha and Jace is an omega, there never was a reason for Alec to think his feelings for Jace were wrong. There was never a reason for the Clave to disapprove, because an alpha loving an omega is the most natural thing imaginable.
So when Jace, eager and bright-eyed, asks Alec to become his parabatai, Alec instead has to ask Jace to become his mate.
- Part 1 of Two Owls
Every Shadowhunter is born either an alpha or an omega. Alec being an alpha and Jace being an omega had from day one taken the connotation of 'wrong' out of his desires for Jace, so when Jace asked him to become his parabatai, Alec countered by asking Jace to become his mate.
That is how Magnus Bane meets them years later; a happily mated pair of beautiful, perfect Shadowhunters. He can't help but slowly fall for them both.
- Part 2 of Two Owls
Covering the second half of season 2, but set in my "Two Owls" verse.
Jace has to face his grandmother, unsure how to tell her that he's dating a warlock.
Magnus has to face the fact that Valentine used his body to hurt one of his boyfriends.
Alec has to face his new grandmother-in-law as well as the responsibilities of becoming co-head of the Institute by mating-status.
Oh, right, and along the way they also still have to stop Valentine and Jonathan.
- Part 3 of Two Owls