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.

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.

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.

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.

Clary and Jace get a tip from Meliorn that they can find Valentine by locating a portal in another dimension, but only Clary can venture into this new world. What Clary finds in this alternative universe is that life there is as if the threat of demons no longer existed and Shadowhunters were no longer needed. While she realizes that this dimension is the life she always dreamed of, Clary must act fast or she will lose herself in the alternative world forever.

Meanwhile, Alec and Isabelle must face the consequences of the Downworlder attack.

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.

The Institute is in full swing as everyone is preparing for the wedding of Alec and Lydia. Lydia is getting final touches made on her wedding dress, the wedding decorations are set and Isabelle is trying to figure out a way to throw a traditional, mundane bachelor party for her brother – whether he likes it or not. During what should be a time of great celebration for many is far from it as they examine their relationships. Alec is struggling on two sides – his wedding is one of the biggest days in his life and his parabatai should be at his side, yet he and Jace are still at odds. Alec also continues to struggle with his feelings for Magnus, especially when Magnus won’t give up on Alec. And as the Institute is buzzing with romance, Clary is desperate to work things out with Jace, but he is keeping her at arm’s length. Meanwhile, Jace, Clary and Magnus go looking for warlock Ragnor Fell to try and find the antidote to awaken Jocelyn.

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.

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.

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.

Already cut off from the Institute and his friends, Jace finds his situation worsen when he becomes a target for the New York wolf pack who believe Jace to be a killer. And don’t forget about Aldertree and the Shadowhunters who continue their own hunt for Jace! With Jace becoming the most wanted man in New York, can his friends get to him before everyone else? Meanwhile, Simon is on a search of his own as Raphael puts pressure on him to find Camille.

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 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.