demands her not to come home, obviously to avoid some type of danger. Clary ignores her mother's warnings and rushes home anyway. Upon her arrival, she finds her mother missing, the apartment trashed, and a monstrous creature (later revealed to being a Ravener demon) waiting. She defeats the creature by shoving a device of Jace’s, called a Sensor, down its throat, but is injured in the process. Jace, who is a demon fighter known as a Shadowhunter, finds her and takes her to his home, called "The Institute." The Institute is an old Gothic cathedral that humans, known by the term "mundanes" or "mundies" in the Shadowhunter world, can't see, because it is shaded from human eyes with magic called glamour. Here, she recuperates; sleeping for three days. After she wakes up, she meets Hodge Starkweather[disambiguation needed], Jace's tutor, as well as his adoptive siblings Isabelle Lightwood and Alec Lightwood.
Hodge then acquires the help of a monk with magical powers, called a "Silent Brother," Jeremiah, to discover how Clary is able to see Shadowhunters despite being a mundane, and why she and her mother were attacked. Jeremiah discovers a block on Clary's mind, keeping her memories sealed, and takes her and Jace to the City of Bones, where the other Silent Brothers attempt to break it. Although the attempt fails, Clary discovers flashes of information, particularly the name Magnus Bane. With Isabelle's help, Clary traces Magnus Bane to a party, which she attends with Jace, Simon, Alec, and Isabelle. There, they discover that Magnus is the High Warlock of Brooklyn, and he placed the block on Clary at her mother's request. Magnus reveals that when Clary was little, her mother, an ex-Shadowhunter, realized she could see creatures of the Shadowhunter world. She initially hoped Clary hadn't developed this ability, known as the Sight, hoping she would live a normal, mundane life. However, when she caught two-year-old Clary trying to play with faeries one day, she realized her daughter would discover the Shadowhunter world if she continued to see its creatures. She went to Magnus with hopes of repressing Clary's memories so she would never discover the Shadowhunter world. She had been sending Clary to Magnus every two years ever since, where he would continue to block her memories and Sight; keeping her in the dark about her true self. Clary, Simon, and the Shadowhunters confront Magnus, asking him to bring back Clary's memories. However, Magnus refuses to bring them back, claiming it will be too difficult, although he says they may slowly come back to her over time, now that she knows the truth. During the party, Simon ignores Isabelle's protests and consumes a drink offered to him by a faerie, which consequently turns him into a rat. He is then abducted by a vampire from Clary's bag, leaving her and Jace to rescue him from a vampire-infested lair.
Clary and Jace are helped into the lair, the abandoned Hotel Dumont, by a teenager named Raphael, who then betrays them, revealing that he is the current leader of the vampire coven that is residing inside that hotel. Soon, Clary and Jace are fighting for their lives. They are saved by werewolves who claim they want Clary, but Clary and Jace escape, and manage to rescue Simon, who eventually returns to his human form. Here she and Simon share an intimate moment where they hug each other in relief for the other's safety; however Jace, upon seeing this moment, "looks away as though the sun is too bright."
At the Institute, while Jace and Simon heal, Clary is approached by Alec in the hallway.
The two begin fighting when Alec demands she return to her own world, claiming she is only hurting Jace by putting him in danger. Clary then reveals that she knows he is gay, and how he feels about Jace - he's in love with him. Alec pins her against the wall, threatening that she'll never reveal his feelings to Jace, before walking off, clearly stunned by his actions. Later, Simon finds Clary and they talk together on Clary's bed before falling asleep in her bed. Clary can't sleep and decides to have a stroll when suddenly she hears someone knocking on her door. Clary finds Jace outside her room looking for her, wanting to take her to celebrate her 16th birthday. He takes Clary to the Institute's greenhouse, where the two talk and eat a meal. He then shows her how the flowers in the greenhouse bloom every night at midnight. They share their first passionate kiss here after Clary nearly steps on the knife that Jace used to cut the apples, but are interrupted by Hodge Starkweather's bird, Hugo. As they return back to her room, Clary and Jace go on to kiss outside the door of the room. However, things are left on something of a sour note when Simon walks in on them kissing when leaving Clary's room, causing Jace to leave. In Clary's room, Simon and Clary argue over her taste in men. However, when Clary brings up Isabelle and how he had been flirting with her, Simon, on impulse, angrily …show more content…
reveals to Clary he had only been trying to get her jealous. Simon then confesses to her how he has been in love with her for over ten years and had only flirted with Isabelle to see how she felt about him back. He says how he's upset that she failed to notice his feelings for her despite how obvious it had been to everyone else.
Later on, while drawing in her sketchbook to calm herself about the night's events, Clary realizes where the Mortal Cup is and she, Jace, Isabelle, Alec, and Simon go and retrieve it at a neighbor of Clary's apartment.
They are attacked by a Greater Demon, but Simon saves them all by shooting an arrow at the roof. Alec gets injured by the Greater Demon and nearly dies, but Magnus Bane manages to heal him at the Institute. When Clary and Jace give the Mortal Cup to Hodge, he reveals he's actually working for a man named Valentine Morgenstern, who is meant to be dead. Valentine kidnaps Jace, saying he was going to take Jace to his father, making Clary fear for him since Jace's father is told to be dead. Clary goes after Hodge who has fled after the kidnapping of Jace, but is knocked unconscious in the process. When Clary wakes up, she finds out her mother's best friend, Luke Garroway is a werewolf and took her away for the sake of her safety. Clary then finds out that Valentine is actually her biological father (her mother having told her that her father was dead when she was little), and Luke and Clary track down Jace and Valentine. Luke and his werewolf pack raid Valentine's lair, but they are
ambushed.
During the attack, Luke and Clary get inside Valentine's lair. While Luke is distracted, Clary finds Valentine and Jace. Valentine reveals to them that he is actually Jace's father as well, making them siblings, shocking and horrifying both Jace and Clary who by then realized that they have fallen in love with each other. Luke then returns to fight Valentine, along with Jace's help, but Valentine escapes to the Shadowhunter capital, Idris, where he has now hidden the Mortal Cup. The Mortal Cup is one of three Mortal Instruments given to the first Shadowhunter by the angel Raziel, and if Valentine has them, he will be able to create a whole army of Demons.
Clary finds her mother, who is in a coma caused by a potion, and takes her to a hospital. In the meantime, Alec has been healed by Magnus Bane and he and Clary decide to start fresh. Afterwards, Clary and Jace meet at the Institute and express their frustration that they cannot be together like they once believed.