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.

To help get answers to what Valentine may be planning, Isabelle and Clary are sent on a mission to visit the Iron Sisters. Once there, more truths may be revealed than Izzy and Clary planned. On a mission of their own, Simon and Maia are determined to find Luke who is still missing after the demon attack at the Institute. Meanwhile, Magnus and Alec finally go on their first date.

Luke’s sister shows up at the Jade Wolf claiming innocence about the recent attack. But with Luke not trusting a word Cleo says, he finds himself at odds with Clary who sees an opportunity to get to Valentine. Yet how far will Clary go to prove she is right about Cleo? Meanwhile, Simon gets dating advice from a surprising source as Isabelle takes a dangerous path.

Tasked with arranging his brother Max’s Rune Ceremony, Alex decides this would be the perfect opportunity for his family to get to know Magnus. But with tensions flying among the different Shadowhunters, Max’s big event quickly becomes an evening where they all must face their biggest fears. Meanwhile, Simon makes a bold move as Isabelle finds an unlikely new ally.

With word getting out that Clary is a key part of Valentine’s plan, the Downworlders are at odds on how to handle the issue. But when Iris activates her blood oath, Clary has more to worry about than hiding from Valentine and the Downworlders. Meanwhile, Isabelle and Raphael get closer as Alec tries to figure out what’s going on with his sister.

The New York Institute is under attack as Valentine’s plan for The Soul Sword is getting dangerously close to coming to fruition. The Shadowhunters must act fast to save their loved ones and the rest of the Downworld. Meanwhile, some of the Downworlders have their own plan to stop Valentine and their target is Clary.

Shadowhunters and Downworlders pick up the pieces after Valentine's attack; Jace carries a heavy burden; a greater demon is loose in Manhattan; Izzy encounters a mysterious stranger; Simon tries to understand his new Daylighter status.

Clary feels pressured between choosing Jace or Simon. Izzy settles things with Raphael. Sebastian breaks his father out of prison.

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

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 everything that Simon has gone through this past year, a family dinner for Yom Kippur – the Jewish Day of Atonement – poses as a real challenge. How can he come clean about being a vampire and especially about what just happened to his family? And if he is stressed out, what if he can’t control his vampire urges? Looking to take care of this himself, Maia insists on helping him out whether he likes it or not. Meanwhile, Clary and Jace go on an unsanctioned mission and test out their newfound rune powers.

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.

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.

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.

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.

Secrets abound as the Shadowhunters and Downworlders try to get back to normal after Valentine's death. Clary struggles with keeping her secret about Raziel's wish, while Alec pushes Jace to come clean about whatever Jace and Clary are hiding. Luke must use tough love to keep his secret hidden from Ollie who is on a war path for answers. And Magnus hides his true feelings about his new position in the Warlock community from Alec. Meanwhile, Lilith sets a plan in motion in New York City as Simon spend stime in the Seelie Court.

The Warlocks’ magic is becoming corrupted by a demonic presence while Izzy and Luke try to track down more information on the recent series of possessions.

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.

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.

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 teams up with Magnus to investigate a recent demon attack. Simon is stunned with he’s visited by someone he never thought he’d see again, and who now won’t seem to leave. Meanwhile, Izzy worries about dinner with her family and a special guest and Luke reaches out to Maryse.

With the Owl's identity revealed, Alec, Isabelle, and Clary head to Alicante to try and find a way to stop him. Luke and Simon team up to track Lilith's latest possible victim. Maia reflects on her past.

Magnus, Alec and Isabelle try to reach Jace inside The Owl, but even as powerful as Magnus is, can he help the Lightwoods retrieve their brother from his demon prison? Maia and Jordan join Simon on the hunt for Lilith, while Luke tries to find a way to get to Clary.

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.

In the climactic mid-season finale, the team scrambles to find a way to put a stop to Lilith’s plan coming to fruition. But going up against their biggest opponent yet, their odds are not looking good. Meanwhile, Simon makes a heartbreaking choice with Isabelle’s help and Magnus reconnects with a powerful person from 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.

Simon is determined to get rid of the Mark of Cain and, with Isabelle’s help, tries to track down New York’s oldest vampire to get more information on the mark. Now in Paris, Clary desperately tries to find an escape from her current situation. Meanwhile, with his new sense of mortality, Magnus tries to live life to the very fullest.

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?

Clary and Jace come up with a risky plan to get rid of her twinning rune, which may bring an old enemy back into the fray. Meanwhile, Alec is worried about Magnus.

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.

A demon outbreak in New York City on Halloween becomes a top priority at the Institute, but as the Shadowhunters hunt the demons, Jace becomes more worried about Clary. Meanwhile, Alec has to juggle the outbreak with his deep concern about Magnus’ depression.

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?

Alec, Jace and Isabelle make a plan to finally get Clary back and stop Jonathan—much to Luke’s and Simon’s chagrin. Meanwhile, an emotionally raw Magnus struggles to deal with his father’s reappearance and Maia must make a tough decision that could affect the rest of her life.

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

Jonathan begins his reign of vengeful terror as the Shadowhunters try to find a way to stop him. With only one hope, Clary must make a sacrifice that could have long-lasting implications for all. Meanwhile, wedding bells are in the air for one special couple.