Sebastian Morgenstern is on the move, systematically turning Shadowhunter against Shadowhunter. Bearing the Dark Cup, he transforms Shadowhunters into creatures out of nightmare, tearing apart families and lovers as the ranks of his Endarkened army swell.
In December 2007, Emma Carstairs is dropped off by her parents at the Los Angeles Institute to train with the other Blackthorn children and their tutor, Katerina, as the Carstairs have been called to investigate demonic activity, while a meeting among the local Conclave takes place at the Institute. In the training room, Emma meets up with her childhood best friend Julian Blackthorn. He is in the midst of annoying his brother Mark, making fun of the latter's name. Ty then throws a knife at Mark, angry that his brother removed the bees he was studying from his room. While Mark tries to appease Ty, Emma and Julian get into a scuffle over her stele. Emma starts to notice his features that have grown more handsome with age, as she lies on top of him. The doorbell to the Institute rings, and a few seconds later the Institute lights up from outside, as if it were on fire. The floor heaves and Emma slides forward, accompanied by a chilling scream. Mark and Katerina go to investigate, leaving Emma and Julian to take care of the twins.
After hearing another scream, Julian decides that it is much too dangerous to remain in the training room. Julian takes Ty and Livvy to the office to send a distress call to the Clave for backup, while Emma goes to fetch the youngest of the Blackthorn siblings - Dru and Tavvy, and bring them to the office. At the nursery, she finds eight-year-old Dru wielding a sword way too heavy to protect Tavvy, who is just two years old, and defenseless. She ushers them out, but in her panic, she takes a wrong turn and ends up at the grand staircase. There, she sees several Shadowhunters, both Conclave members, and Endarkened. In the midst of them all is Sebastian Morgenstern, carrying the Infernal Cup. Sebastian hasn't yet noticed her, and orders Julian's father - who is now Endarkened - to bring forward Katerina. Emma witnesses Katerina drink from the Infernal Cup, and she too turns Endarkened. Katerina brings forward Mark, and Sebastian decides he doesn't want him, and asks Mr. Blackthorn to wound him. Emma tells Dru and Tavvy to flee to the office, and she throws a knife at Sebastian. Though the aim is true - it hits his heart - he doesn't die; instead he laughs, and sets his warriors on her. Emma turns and sprints towards the office, where Julian is waiting for her besides an open Portal. The pair jump through just as the door bursts open an the Endarkened flood the room, and the Portal closes behind them.
Jace Lightwood meets with Jordan Kyle in Central Park so that Jordan can help him learn to meditate, in an effort to help control his heightened emotions resulting from the heavenly fire in his veins. It doesn't work very well, as Jace's life has been brought up a warrior and war is what brings him peace. After Jordan leaves to meet Maia, Jace joins Clary, Simon, Isabelle, and Alec, who were hanging out nearby for moral support. Alec is staring at his phone, pining over Magnus as it is the warlock's birthday. Jace breaks his phone to prevent Alec from texting Magnus anymore, making Alec frustrated and annoyed. Isabelle informs the group of the Clave meetings that have occured since the Battle of the Burren; the Shadowhunters wanting to know everything about Sebastian. They discuss the Claves refusal to believe that Sebastian and his Endarkened are a threat, and the efforts being made to track Sebastian, and reverse the effects of the Infernal Cup, while the Iron Sisters are making weapons by the dozen. Isabelle gets a call from her mother, instructing her and Alec to return to the Institute for a meeting; she then convinces Jace to go to Magnus's apartment to talk to him about Alec, while Clary and Simon go Christmas shopping.
While shopping, Clary and Simon reminisce about the times when they were unaware of the Shadow World, and discuss the state of Simon's relationship with Isabelle, and she encourages Simon to make things official with her. Clary says that she can never forgive Sebastian, and Simon worries about his future as a vampire, and Clary urges him to talk to Raphael Santiago. They are found by Jocelyn and Luke, who-after fussing over Clary-drags her away to attend the emergency meeting at the Institute.
Meanwhile, Jace tries to get Magnus to get back together with Alec. He argues that Alec is miserable, and Magnus is too, evident by the sorry state of his apartment. When Magnus disagrees, he interrogates Magnus about his life, which Magnus doesn't answer. Jace is about to settle down-trying to prove he has all the time in the world-when Izzy calls, asking him to return to the Institute for the meeting, which has something to do with Sebastian. Magnus is worried is Alec is all right, and Jace asks him why he cares, and leaves.
At the Institute, the New York conclave have a meeting in the library. Maryse reveals that six institutes have been attacked over six days, with all the Shadowhunters either killed or Turned, with the exception of the Blackthorn children, who made it safely to Idris. Jace arrives and Maryse confirms that the attacks were Sebastian's doing. Jace accuses the Conclave of not listening to his warnings to ready more soldiers. Maryse instructs them all to pack their bags, as all the Shadowhunters in the city would be Portalling to Idris that night, after which the wards around Idris would be doubled, allowing no one to enter or leave.
In Idris, Emma wakes up in a bed in the attic of the Penhallow's home, where Helen Blackthorn is checking on her. She immediately asks where her parents are, but Helen ignores the question in favor of filling her in on the rest of the details she missed while she was unconscious; that all the Blackthorn children made it to safety, and that Sebastian was behind the attacks of six Institutes. Emma tells her what happened to Helen's father, Mark, and Katerina, and a visibly distressed Helen informs Emma of her parent's death. A shocked Emma begins to scream, and is only able to stop when Julian rushes in with Cortana. Emma hugs Cortana close to her, seeking comfort from the blade and uncaring that it is cutting her arm.
The next day, Catarina Loss, who is filling in for Magnus so he wouldn't have to see Alec, helps the New York Conclave create a Portal to Alicante for the emergency Clave session. Clary and Simon say their goodbyes, with Clary urging Simon to talk to Izzy and Simon reassuring her that he would be safe with Jordan. Clary leaves Simon to say bye to Izzy. Magnus also arrives to talk to Alec, who is so nervous that he is speechless. They share a kiss, which Magnus regrets, and Alec reminds him that their breakup was both their faults. Magnus leaves after telling Alec to stay safe and alive.
Simon and Isabelle talk across the courtyard, with Simon wishing that he was accompanying her to Idris and Izzy telling him he is safer in New York. They indirectly admit their love for each other. Izzy, after giving him her ruby necklace to protect him, leaves to enter the portal.
Clary, Jocelyn, and Luke arrive at Amatis's house in Idris, where CLary heads up to the spare room. She looks through Amatis's chest of clothes and stumbles on a white mourning dress, which Jocelyn encourages her to wear as a show of solidarity for the killed Shadowhunters. She sleeps fitfully for a few hours, and then wakes to get a glass of water. She ends up eavesdropping on Jocelyn and Luke, the former telling Luke that she found the box in which she had kept Sebastian's photos and clothes. Jocelyn confesses that she wishes she had killed him when she had the chance.
The next morning, on the way to the meeting Clary tells Jace about the conversation she overheard. Jace replies that he thinks Sebastian left the box as a message when he took Amatis from her house. The meeting begins on the topic of the Endarkened, and whether they can be turned back to normal. Jia asks Helen to bring out Julian and the rest of the Blackthorn children to give testimony to the events at the Los Angeles Institute. Julian takes the Mortal Sword and recounts the events of the previous day. Emma, seeing that remembering his brother Mark and his father hurts him, begs them to stop and takes the sword herself. She tells them her side of events and Sebastian's messages, and then runs away, hurt that they're torturing them. Clary runs after her and meets Aline, who tells her that Emma doesn't have a family left. Clary talks to Emma, and compliments her sword and her friendship with Julian, which reassures the young girl. When Jace arrives, Emma recognizes Clary for who she is, and tells her to get a better sword.
At the Lightwoods' new home in the city, they discuss the next course of action for the Shadowhunters, Alec believing they will win seeing that they have the Downworlders at their side, despite Clary and Jace being skeptical. Jace fills in Clary on the events of the meeting, which spoke about him and his heavenly fire. When Alec brings up their parents' separation and Max's death Isabelle storms off, leaving Jace to walk Clary back home.
Back in New York, Maia, Jordan, and Simon are hanging out at Jordan's apartment, waiting for their take out. They discuss Simon's life, and the state of the city's downworld. The take-out arrives, and just before Simon opens the door, Izzy's necklace pulses, giving him a second to jump away from the Endarkened who storm the apartment. Simon escapes down the fire escape as Maia and Jordan fight them. He ends up in the midst of vampires, led by Lily and Zeke, who capture him.
In Alicante, as Jace walks Clary back to the house, they discuss Emma, Clary stating she likes the girl because she reminds her of Jace. They end up in an alley, where despite Jace's hesitation, they make-out. It escalates, Jace losing control of the Heavenly Fire and burning handprints into the brick wall. He panics and pulls away from Clary out of fear from hurting her.
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