With Valentine in custody and the Shadowhunters and Downworlders picking up the pieces after the Soul Sword attack, the team dive into a new mission to vanquish a greater demon named Azazel who is in search of the Mortal Cup.
The New York Institute is under attack, as Valentine's plan for the Soul Sword gets dangerously close to coming to fruition. The Shadowhunters must act fast to save their loved ones; and some of the Downworlders have their own plan to stop Valentine, and their target is Clary.
The Downworlders are at odds on how to handle the issue of Clary being a key part of Valentine's plan, but when Iris activates her blood oath, Clary has more to worry about than hiding from Valentine and the Downworlders. Meanwhile, Isabelle and Raphael get closer, as Alec tries to figure out what's going on with his sister.
Alec and Magnus host a celebration in honor of Max's first rune, but the event provokes everyone's fears as tensions amongst them continue to rise. Meanwhile, Simon makes a bold move; and Isabelle finds a new ally.
Luke's sister claims that she wasn't involved in the recent attack, and although Luke doesn't trust her, Clary believes her and sees an opportunity to reach Valentine. Elsewhere, Simon receives dating advice; and Isabelle takes a dangerous route.
Clary and Isabelle visit the Iron Sisters in search of information regarding Valentine's plan. Elsewhere, Simon and Maia search for Luke, who went missing during the attack on the Institute; and Magnus and Alec go on their first date.
Jace awaits his trial in the City of Bones. Elsewhere, Clary fights against a demon who's terrorizing the Institute with Alec and Isabelle; Jocelyn confronts Clary with a proposition; and Raphael and Simon take their hunt for Camille to another level.
Alec and Isabelle race to find Jace before the other Shadowhunters locate and kill him. Meanwhile, Simon seeks Magnus' help when he finds himself at odds with Raphael and Aldertree; and Clary struggles to fit in while longing for her old, mundane life.
In the Season 2 premiere, the Institute is left in a state of disarray following Jace's departure with Valentine. Meanwhile, Clary, Isabelle and Alec are determined to find Jace, but the arrival of Victor Aldertree hinders their investigation; and Jocelyn must catch up on everything she missed while asleep.