Clary Fray is thrown into the world of demon hunting after her mother is kidnapped, and must rely on the mysterious Jace and his fellow Shadowhunters Isabelle and Alec to navigate this new dark world. With her best friend Simon in tow, Clary must now live among faries, warlocks, vampires and werewolves to find answers that could help her find 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.
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.
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.
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.
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. Magnus and Luke reveal Clary's past. Meanwhile, Isabelle and Alec are tasked to restore their family name in the eyes of The Clave.
The Mortal Cup is within Clary's grasp. Armed with the knowledge of the Mortal Cup's location, Clary and the team race to get it before anyone else. 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.
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.
With the help of a new ally, Clary and Jace attempt to rescue Jocelyn 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.
On the eve of Alec and Lydia's wedding, relationships are examined. 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.