Jace’s concerns grow about his mental state and turns to Luke for information on his family’s past. Clary and Izzy go after a rogue vampire and Simon hunts for a new apartment.

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 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.

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.

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.

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 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 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 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.

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.

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.

The Shadowhunters try to track down the new imposing threat, while Jace has a suspicion that Jonathan is back and behind the mundane attacks. Simon tries to figure out what The Seelie Queen did to him during his time in the glade. Alec decides to host a Lightwood family dinner at Magnus’ house after a surprising visit from Maryse.

Someone is out to get Simon and Jace is on the hunt to find out who it is, meanwhile Clary turns to Luke to find a way to help Jace. Alec worries about the future of his relationship after learning more about Magnus’ romantic past.

Clary faces down an old foe in an attempt to find answers about Lilith’s plan. Alec and Magnus turn to Lorenzo Rey for help, while Lilith finds a new ally. Luke must choose between his pack and his family, as Simon is forced to deal with his past.

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.

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.

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.

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?

Simon and Izzy team up on a secret mission to figure out what the Clave is hiding. Meanwhile, Clary is conflicted about Jonathan as the Shadowhunters try to get answers.

To try and save Clary from Jonathan, Jace goes undercover. Back at the Institute, Isabelle, Simon and Luke race to find a way to finally destroy Clary’s bond with Jonathan. With time running out, can Isabelle create the solution before Jace’s cover is blown?

Clary comes up with a plan that will bring Shadowhunters and Downworlders together, as Alec struggles for a way to help Magnus.

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.

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