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.

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.

One young woman realizes how dark the city can really be when she learns the truth about her past.

With the knowledge that Valentine is alive and on the hunt for The Mortal Cup, the Institute is on high alert. Not wasting any time, Jace jumps into action and figures Clary’s memories are the key to finding Jocelyn and The Mortal Cup. Unfortunately, Clary’s memories were wiped leaving her without any recollection of this other life that could help her and the team. With only one other option remaining, Jace, Isabelle and a very reluctant Alec take Clary to the City of Bones to face the powerful Silent Brothers. Meanwhile, Luke continues his search for Clary, and Simon tries to come to terms with his best friend’s new life.

With Simon being held captive at The Hotel DuMort, Clary pleads with Jace, Alec and Isabelle to help her rescue her best friend. As the team readies for the mission, Jace helps Clary learn more about her Shadowhunter powers, Isabelle turns to her favorite Seelie for Intel, and Alec begins to question Jace's motives and his place in their partnership. Meanwhile, a very scared Simon gets very up close and personal with Camille, the leader of the vampire clan.

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.

The hunt is on for Jace Wayland, and Alec and Isabelle hope to reach him before the rest of the Shadowhunters do. With orders from the Clave of “shoot to kill,” the Lightwood siblings must act fast. Also on his own search, Simon turns to Magnus for help when he finds himself at odds with both Raphael and Aldertree. Meanwhile, Clary struggles to find where she belongs since she doesn’t seem to fit into the Shadowhunter world, yet can’t go back to her mundane life.

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.

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. Meanwhile, Jocelyn has a proposition for Clary as Raphael and Simon ramp up their hunt for Camille.

After a devastating attack at The Institute, everyone is on high alert as the Shadowhunters close in on their hunt for Jonathan; Simon and Maia help a new Downworlder as the Seelie Queen demands an answer from Magnus and Luke.

Jordan and the Praetor try to track down Heidi, while the Shadowhunters try to locate Jonathan. Meanwhile, Luke looks to Maryse for help and Isabelle gets a possible lead on information on what is really going on in the Clave prisons.

After getting a clue about who may have wiped Clary's memories, the crew hunts down the High Warlock of Brooklyn, Magnus Bane. With all of the warlocks in hiding from Valentine, the team must lure Magnus out with something he can't refuse - a killer party and something very valuable. But with emotions running high, more may come out of their meeting with Magnus than just the retrieval of Clary's memories. Meanwhile, Simon doesn't seem to be himself after his recent Downworlder encounter.

Tensions escalate between Alec and Clary as they don't see eye to eye on the best way to hunt down Valentine. But when Jace and Isabelle are sent on an intel mission to the Seelies by Maryse Lightwood, Alec is put in charge of keeping Clary safe, much to both of their chagrin. With his hard-as-nails mother back in town and Clary's rule-breaking tendencies, Alec finds himself struggling to stick to the Claves rules while keeping his promise to Jace. Meanwhile, the New York City Werewolf pack begins their hunt for Clary and The Mortal Cup.

After several Shadowhunters are killed, The Institute turns to controversial methods to prevent a Downworlder uprising.

Continuing to track down information on the rumors about misconduct at The Clave’s downworlder prison, Isabelle asks Alec for help. Meanwhile, Magnus succumbs to asking Lorenzo for a favor and Jace takes Clary on a special date.

With word of Alec, Jace and Isabelle’s “extracurricular activities” with Clary reaching The Clave, a convoy is sent to observe the Lightwoods running the New York Institute. Once The Clave representative arrives, it is very clear how much trouble the Lightwoods are in. Meanwhile, Clary is faced with a devastating decision.

Jace, who is still reeling from everything that has happened, makes hunting down Valentine his number one priority even though he continues to wrestle with his conflicted feelings. In hopes of finding a way to stop Valentine before it is too late, Clary and Simon must find the key to unlocking Jocelyn's coma. But that key to unlocking Jocelyn’s spell may just undo the Downworlder peace treaty, Simon's relationship with Raphael, and the Vampire clan in the process. Meanwhile, Alec must deal with the aftermath of his decision and what his choice means for his future.

As the saying goes, “rules are made to be broken.” But what if the rules are there for a reason? Several members of the team must examine the reasoning behind certain rules after consequences to questionable actions come to light. Whether the rules were broken because of love, loyalty or revenge, does the end justify the means?

With Luke in dire need of help, Jace, Clary and Simon take him to Magnus' lair in hopes of saving his life. Once there, the story of how Valentine came to be evil, and Jocelyn and Luke's past is revealed to Clary in hopes of triggering her memory of what happened to The Mortal Cup. Meanwhile, Isabelle and Alec are tasked to restore their family name in the eyes of The Clave.

After the attack, the Institute and The Clave are on high alert and taking no prisoners to get answers. When Lydia makes a harsh call on the Seelies, Jace, Clary and Isabelle fear that this decision could be disastrous and the wrong way to defeat Valentine. Left with no other choice, the trio takes drastic actions to stop what is about to take place. Meanwhile, Simon struggles to deal with his new situation, and Alec is emotionally torn with what is happening at the Institute.

After receiving important intel about Valentine from a surprising ally, Clary, Jace and Luke devise a plan to rescue Jocelyn. With the mission looking almost impossible, the three will stop at nothing to rescue Clary’s mother and put a stop to Valentine once and for all. Meanwhile, Inquisitor Herondale arrives at the Institute for Isabelle’s trial as Alec turns to Magnus for help.

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.

Alec has big plans to mend fences with the Downworlders, while Jace and Clary are summoned by the Seelie Queen.

Simon goes down a dark path while Alec and team prepares to transport Valentine.

With the loss of Clary after Lilith’s apartment exploded, Alec, Isabelle and Jace try to come to terms with what has happened. Glad to have their brother back, Alec and Isabelle are still worried about Jace, who is taking the actions of The Owl very hard. Magnus is also mourning the loss of his magic and finds himself in a new position—having to rely on others for help. Meanwhile, Maia tries to help a devastated Simon who has lost his family and his best friend. But unknown to everyone, Clary is alive and finds herself in a new and dangerous predicament.