Based on the bestselling young adult fantasy book series The Mortal Instruments by Cassandra Clare, Shadowhunters follows 18-year-old Clary Fray, who finds out on her birthday that she is not who she thinks she is but rather comes from a long line of Shadowhunters - human-angel hybrids who hunt down demons. When her mother, Jocelyn, is kidnapped, Clary is thrown into the world of demon hunting with mysterious Shadowhunter Jace and her best friend, Simon. Now living among faeries, warlocks, vampires and werewolves, Clary begins a journey of self-discovery as she learns more about her past and what her future may hold.
Only hours have passed since Jace left with Valentine and all hell has broken loose at The Institute. Alec, Isabelle and Clary are desperate to find Jace, but are quickly stopped in their tracks with the arrival of Victor Aldertree, who means business about getting the Institute back on track. But getting the New York Shadowhunters in-line with The Clave may be counterintuitive to Alec, Isabelle and Clary's plan to rescue Jace. Meanwhile, Jocelyn has a lot to catch up on now that she is awake.
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.
Clary continues to struggle with the new Shadowhunter order as Jace is being held in The City of Bones with an unknown fate, and all suspicion in the Shadowhunter world continues to rest on Valentine's daughter. When duty calls, Clary gets a little reprieve from the family drama as she helps Alec and Isabelle hunt down a powerful demon. But what starts out as a routine mission quickly puts the Institute on high alert, and what happens next will change everything for the Shadowhunters and their Downworlder friends.
After the recent attack on the Institute, the Shadowhunters are left devastated and wounded. Trying to regroup, each of the Shadowhunters deals with the situation their own way. Meanwhile, Simon moves home but finds it is not so easy to pull off his new life with his family around.
To help get answers to what Valentine may be planning, Isabelle and Clary are sent on a mission to visit the Iron Sisters. Once there, more truths may be revealed than Izzy and Clary planned. On a mission of their own, Simon and Maia are determined to find Luke who is still missing after the demon attack at the Institute. Meanwhile, Magnus and Alec finally go on their first date.
Luke's sister shows up at the Jade Wolf claiming innocence about the recent attack. But with Luke not trusting a word Cleo says, he finds himself at odds with Clary who sees an opportunity to get to Valentine. Yet how far will Clary go to prove she is right about Cleo?
Meanwhile, Simon gets dating advice from a surprising source as Isabelle takes a dangerous path.
Tasked with arranging his brother Max's Rune Ceremony, Alex decides this would be the perfect opportunity for his family to get to know Magnus. But with tensions flying among the different Shadowhunters, Max's big event quickly becomes an evening where they all must face their biggest fears.
Meanwhile, Simon makes a bold move as Isabelle finds an unlikely new ally.
With word getting out that Clary is a key part of Valentine's plan, the Downworlders are at odds on how to handle the issue. 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.
With everything that Simon has gone through this past year, a family dinner for Yom Kippur - the Jewish Day of Atonement - poses as a real challenge. How can he come clean about being a vampire and especially about what just happened to his family? And if he is stressed out, what if he can't control his vampire urges? Looking to take care of this himself, Maia insists on helping him out whether he likes it or not. Meanwhile, Clary and Jace go on an unsanctioned mission and test out their newfound rune powers.
With two of the three Mortal Instruments missing, everyone is on the hunt for the last one - The Mortal Mirror. Jace and Clary are on the hunt to recover it first before it could fall into enemy hands. But along the way, Clary realizes that her brother Jonathan may be closer than she thought. Meanwhile, Isabelle has a hard time accepting the fact that her little brother Max is growing up, and Maia struggles to bring her guard down with Simon.
After a devastating attack at The Institute, everyone is on high alert as the Shadowhunters close in on their hunt for Jonathan. Meanwhile, Simon and Maia help a new downworlder as the Seelie Queen demands an answer from Magnus and Luke.
After centuries of being lied to and treated poorly by The Clave, the Downworlders decide to come together and take matters into their own hands as the hunt for Valentine and Sebastian intensifies. But what starts off as a way to preserve their own, the Downworlders choice to break with the Shadowhunters, could quickly escalate to war.
Jace and Clary rush to make a final stand, but when a traitor is revealed, Jace and Clary may have a bigger fight on their hands than expected. Meanwhile, Alec and Izzy must fight off a large mass of demons that have unexpectedly shown up, as Luke and Simon head to the Seelie Court to deal with some unfinished business with the Seelie Queen.