Magnus and Alec have been secretly dating, even though Alec still thinks he is in love with Jace.
Alec refuses to tell others about the relationship due to how homosexuality isn't approved
among Shadowhunters, often resulting in them being kicked out. Magnus takes Jace in to his
apartment when he is injured. Magnus is upset by this and nearly tells Jace of his relationship
with Alec, but ends up deciding against it knowing that Alec isn't ready for that kind of step
yet. In a chapter of the novel, Clary creates a "fearless" rune , which Alec volunteers to have
applied to his arm in order to test it to see if it works. In result of applying the rune, he nearly
openly tells his parents about his relationship with Magnus as well as his homosexuality,
shocking those who are aware of it. However, before he can directly reveal who he is seeing
and the importance of it, Magnus quickly uses a spell to momentarily knock Alec unconscious
and from revealing their relationship, knowing Alec isn't ready for anyone to know about them
yet.