London, April 1878. Shadowhunter William Herondale kills a Shax demon and searches for Jem his "hunting buddy" (parabatai). Jem is in an alley and has found the body of fourteen-year-old Emma Bayliss. They find a dagger imprinted with two snakes each biting the other's tail, an ouroboros.
Southampton, May. Tessa is thinking of her clockwork angel necklace when she arrives at Southampton dock aboard the Main, expecting to find her brother Nate waiting for her. Tessa was living in NY with her Aunt Harriet, but her aunt had passed away recently and her brother asked her to come stay with him in Liverpool. At the port, instead of her brother, Tessa finds the Dark Sisters, Mrs. Dark and Mrs. Black, who have a letter from her brother saying that he could not meet her because of business, but that the sisters will bring her to him. Tessa goes with them.
Six Weeks Later. Tessa has been held prisoner by the Sisters. They have been training her to Change (a process by which she takes on the appearance of someone else, living or dead, by holding something which belongs to them). This time Tessa becomes Emma Bayliss and relives her last few moments alive. The sisters are impressed and tell Tessa that they have been preparing her for an arranged marriage to a mysterious individual known as "the Magister." The expect the marriage to take place that day or the next. The sisters leave and Tessa tries to run away but is caught by the Sister's coachman. Tessa is tied to her bed, she attempts to escape again by using the Change. Just as she escapes her bindings the door opens. It is Will, who followed the trail from Emma's body to an organization called the Pandemonium Club and the Sister's house. Will and his friends proceed to help Tessa escape and when the Dark Sisters catch up a battle begins in which Mrs. Black is killed, and Tessa is knocked unconscious.
Tessa awakens in the London Institute to find herself being examined by Brother Enoch, one of the Silent Brothers, who informs her that she is a shape-changer and a Downworlder. Tessa meets the inhabitants of the Institute. The next morning Jessamine takes Tessa shopping; Charlotte and Henry look for Tessa's brother; and Will and Jem inspect the Sister's house. Will and Jem find a clockwork automaton wrapped in human flesh. A vampire named de Quincy is identified as the Magister and is said to have Tessa's brother. Tessa and Will infiltrate one of de Quincy's parties. At his parties de Quincy slowly drains a human victim; this is against the Accord, which allows the Shadowhunters to attack de Quincy. Things go terribly wrong at the party when de Quincy's victim is revealed to be Tessa's brother Nate.
Tessa and the Shadowhunters kill the vampires at the party, save Nate and bring him to the institute, but de Quincy escapes. Will bites a vampire, while fighting, and accidentally swallows some of the vampires blood. To get the blood out of his system, so he won't turn into a vampire, has to drink holy water. When Tessa brings him a bucket of holy water they kiss. Tessa and Jem go for a walk and are attacked by the Magister's clockwork army. They make it to the institute where the Shadowhunters barely fight the army off. Jem reveals that he is addicted to demon blood and is slowly dying from it. Most of the Shadowhunters leave to kill de Quincy who is hiding out. Mortmain, the mundane who informed the Shadowhunters of de Quincy comes back to the institute and tells Will and Jem the location of the Dark sister who is trying to help the Magister with his army. They rush off to kill her leaving Nate, Jessamine and Tessa alone. Mortmain comes back with the clockwork army and reveals himself as the real Magister. Nate reveals himself as Mortmain's accomplice. The girls lock themselves in a room, but Mortmain tricks them to open the door. Tessa agrees to marry Mortmain if he will leave everyone alone and he agrees. Once the army has left the room Tessa stabs herself in the heart and Mortmain leaves.
Will rushes back when he realizes his mistake. At the Institute he runs into the army and Nate. Nate orders the army to kill Will. Jem makes it back and helps Will and then the rest of the Shadowhunters arrive. The army leaves. Will finds Tessa who is alive; she Changed quickly just before stabbing herself and the blood was from a gunshot victim she had Changed to before with the Sisters. Tessa is asked to stay at the Institute and she happily accepts. Tessa wants to have a serious relationship with Will, but he says that she cannot have children (she is a warlock) so it is impossible. Jem comforts her though she will not tell him exactly what Will did to annoy her. Will seeks Magnus Bane's help, but it is not revealed for what reason.