18-year-old Clary Fray finds out that she 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.
On her birthday, Clary Fray finds out 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. After her mother is kidnapped, Clary must rely on the mysterious Jace and his fellow Shadowhunters Isabelle and Alec to navigate this new dark world filled with faeries, warlocks, vampires and werewolves to find answers that could lead to her mother.
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.
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.
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 piecing together the clues as to where her mother hid the Mortal Cup, Clary, Jace, Alec and Isabelle are on the clock to find its hiding place before anyone else. But with demons and Downworlders lurking everywhere, obtaining the Cup may not be as easy as they had hoped. Meanwhile, as Simon’s symptoms become increasingly worse, he fears he is turning into a vampire.
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.
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.
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, and Isabelle is trying to figure out a way to throw a traditional, mundane bachelor party for her brother. Alec is struggling on two sides – his parabatai should be at his side on his wedding day, 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. Meanwhile, Jace, Clary and Magnus go looking for warlock Ragnor Fell to try to 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.