The following version of the book was used to create this study guide: Clare, Cassandra, et al. Ghosts of the Shadow Market. Simon and Schuster Children's Publishing, New York, New York, 2019. Kindle AZW file.

The novel opens in 1901 with a story titled “Cast Long Shadows.” Brother Zachariah, a member of the Silent Brothers, spending time in a Shadow Market. He was a Shadowhunter named Jem Carstairs until he almost died due to an involuntary addiction to a drug called yin fen. He became a Silent Brother, a race of immortals that provides various services, including tending the sick, wounded, and dead. Shadow Markets are where Downworlders (faeries, vampires, werewolves, and the like) gather to buy and sell, so Brother Zachariah is surprised when encounters a young Shadowhunter named Matthew Fairchild. Matthew has recently begun to doubt that his father is his biological parent, and is searching for a potion that would force her to tell the truth. He manages to buy the item while Brother Zachariah is not watching and gives it to his mother. Within seconds, she collapses and Matthew learns that his father really is his biological parent, and that his mother was expecting another child until the potion caused her to miscarry. Brother Zachariah tends Matthew's mother and, knowing what happened, encourages Matthew to tell the truth. He feels he can never tell anyone.

The next story, “Every Exquisite Thing,” takes place later that year. Brother Zachariah encounters Anna Lightwood and Ariadne Bridgestock outside a home where a warlock woman conjures demons that kills several humans. He steps in to help Anna and Ariadne, then sends them home while he has the warlock killed. Anna has decided she enjoys the power she feels when she wears men's clothing and she has fallen quickly in love with Ariadne, who seems to return the feeling. Ariadne, however, has agreed to begin courting Charles Buford, Matthew Fairchild's brother, to avoid the stigma of being gay in this society. While Anna's heart is broken over this, she is happy when her parents present her with a gift – a complete outfit of stylish men's clothing – and make it clear they support her decision.

The next story is titled “Learn About Loss” and takes place in Chattanooga, Tennessee, in 1936. Brother Zachariah and Sister Emilia of the Iron Sisters are on a mission to shut down an illegal Shadow Market that is operating in full view of normal humans, or mundanes. They quickly discover a demon named Belial is at the heart of the market. The demon offers Brother Zachariah a choice – the location of Shadowhunter descended from the Herondales who has been out of contact for a long time and is in danger, or details of how to cure Brother Zachariah of his yin fen addiction, meaning he could become human again. Though he desperately wants to be human, he chooses the former and rushes to try to save the Shadowhunter, a man he saw earlier but without recognizing him.

The next story is titled “A Deeper Love” and takes place four years later in London. Tessa Gray, the woman Jem loved and that Brother Zachariah desperately wants to return to, is working as a nurse in war-torn London. She is immortal and is working alongside another immortal, Catarina Loss. One evening, Brother Zachariah is following yet another lead in the hope of finding the lost Herondales when a Downworlder stabs him. He can feel the poison moving into his body and though Silent Brothers are immortal, they are not invincible. Brother Zachariah knows that Tessa is the only one who can help him and she and Catarina spend a night tending his wounds.

The next story is titled “The Wicked Ones” and takes place in Paris in 1989. A man named Valentine Morgenstern is recruiting young Shadowhunters with plans to launch a coup. One of them is Celine Montclaire who has a crush on Stephen Herondale. She is horrified when she overhears Stephen calling her a child he could never take seriously. Valentine tells Celine she is special, reveals more of his plan to her than he does others, and pledges that she and Stephen will be together if she gives her loyalty to Valentine's plans. She does.

The next story is titled “Son of the Dawn” and takes place in New York City in 2000. Celine and Stephen's son, Jace Herondale, is an orphan traveling to live with Robert Lightwood's family. He is aboard a ship crewed by werewolves transporting the drug yin fen into the city. Brother Zachariah brokers a joint effort between local vampires and Robert, and they intercept the drugs, killing the crew in the process. Jace, who had a brutal childhood, is quickly embraced into the Lightwood family, especially by Alec who becomes Jace's parabatai.

The next story is titled “The Land I Lost” and opens in New York in 2012. Alec and Jace are settled in as leaders among the Shadowhunters. Alec is living in a committed relationship with warlock Magnus Bane and they have a son named Max. Brother Zachariah has transformed from a Silent Brother to his human form and is married to Tessa Gray, a shape-changer he has loved for decades. Jem and Tessa call on Alec to help solve the mystery of werewolves vanishing in Buenos Aires and to find new information about the missing Herondale descendant. They solve both mysteries, discovering that the first Herondale descendant – Roland – married a faerie who was prophesied to be the one to bring an end to the faerie land. Alec also discovers the local Shadowhunter Institute is filled with corruption and puts a stop to that while rescuing a young Shadowhunter orphan and setting out to adopt him into his family.

The next story is “Through Blood, Through Fire” and is set in 2012. In this story, Tessa and Jem locate Rosemary Herondale, the direct descendant of Roland Herondale and the faerie predicted to bring ruin to the land. They are not able to save Rosemary but do rescue her son, Kit, and settle him in at a Shadowhunter Institute. Meanwhile, Tessa announces she is expecting a child.

The next story is titled “The Lost World” and is set in 2013. Ty Blackthorn tried to resurrect his dead sister Livvy, but managed only to bring her back as a ghost. They are currently testing the limits of the bond between them and discover that they have to remain physically near each other for Livvy to retain her humanity.

The final story is called “Forever Fallen” and it takes place in New York in 2013. In this story, a character named Janus is present from an alternative universe where he is Jace Herondale. He has entered into a deal with faeries and has spent years training and raising a faerie named Ash. In his world, many of the people he loves are dead, including Clary, and Janus plans to murder the Jace of this world and step into his place. He has a chance to interact with Clary for a few minutes and it is clear she feels there is something wrong. Realizing this plan will not work, Janus returns to Ash, working out a new plan for the future.