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. (Guest starring Anna Hopkins, Chai Hansen, Alexandra Ordolis and Nicola Correia-Damude)
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. (Guest starring Anna Hopkins, Chai Hansen and Javier Muñoz)
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. (Guest starring Anna Hopkins, Jack Yang, Alexandra Ordolis and Nicola Correia-Damude)
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.