City of Glass recap

Told that only a warlock in Idris can wake her mother, Clary follows the Lightwoods to the Shadowhunter homeland after Jace tries to leave her behind, and arrives by a Portal of her own making. In Alicante she is taken in by Luke's estranged sister Amatis, Simon is imprisoned for being a vampire on Shadowhunter soil, and she is befriended by a visiting Shadowhunter named Sebastian Verlac. Searching for the spellbook that will wake Jocelyn, she and Jace find an angel chained beneath Valentine's old country house whose visions reveal that Valentine experimented on unborn children with angel and demon blood. Sebastian sabotages the city's defences, kills the Lightwoods' youngest son and is exposed as Jonathan Morgenstern, Valentine's true son. Clary invents a rune that lets Shadowhunters and Downworlders fight as bound partners, and the Clave accepts the alliance. Jace kills Sebastian on the battlefield, and Valentine kills Jace at Lake Lyn to summon the angel Raziel, only for Clary to have rewritten the ritual in her own name. Raziel destroys Valentine and restores Jace. Jocelyn wakes and confirms that Jace is a Herondale, not her son, and that Clary and Jace were never siblings.

Clary Fray discovered she was a Shadowhunter after seeing a demon killed in a nightclub and losing her mother Jocelyn the next day. Her father is Valentine Morgenstern, who once led the Circle in an attempt to purge the Downworlder races and overthrow the Clave, and who faked his own death. Valentine took the Mortal Cup, then slaughtered the Silent Brothers to take the Mortal Sword and corrupted it into a demonic instrument aboard his ship, from which he escaped when Clary destroyed the vessel with a rune of her own invention. Only the third Mortal Instrument, the Mirror, is still unaccounted for, and nobody knows what it is. Valentine told Jace and Clary that he is father to both of them, so the two believe themselves to be brother and sister; Jace was raised by Valentine under another man's name and has been mistrusted by the Clave ever since the truth came out. The Inquisitor Imogen Herondale died defending him. Jocelyn lies comatose in a Manhattan hospital after drinking a potion to keep herself out of Valentine's hands. Clary's oldest friend Simon was killed and rose as a vampire, and after drinking Jace's blood became a Daylighter, able to walk in sunlight, which no vampire has ever done. Luke, once the Shadowhunter Lucian Graymark, leads a Manhattan werewolf pack and looks after Clary in her mother's place.

A former Circle member named Madeleine finds Clary and tells her that Jocelyn's coma is self-inflicted and can be undone, but only by a warlock living in Idris, the Shadowhunter homeland. Madeleine is killed before she can help further. The Lightwoods are being recalled to Alicante as the Clave gathers against Valentine, and Clary intends to travel with them, but Jace disables the Portal behind him rather than let her follow into a war. Clary makes her own Portal instead and comes through with Luke and Simon, falling into Lake Lyn on the way; the water of that lake is poison to Shadowhunters and leaves her ill and disoriented. Luke's estranged sister Amatis takes her in, and the reunion between Clary and Jace is furious on both sides.

Alicante is a city with demon-repelling towers and a hard rule against Downworlders, so Simon's arrival is treated as a crime. He is imprisoned in the Gard and questioned by the new Inquisitor, Aldertree, who starves him and offers to trade his freedom for testimony against the Lightwoods. Clary, staying with Amatis, is taken to meet the Penhallow family and is befriended by Sebastian Verlac, a Shadowhunter of her own age from the Paris Institute whose household was destroyed. He is charming and helpful, and Jace dislikes him immediately. The Clave debates Valentine's demand that it submit to him, and refuses to consider arming Downworlders.

Clary rides out with Sebastian to find the warlock who can wake her mother and discovers he is dead, killed by Valentine's demons; Magnus Bane is waiting in his place. Magnus tells her the antidote cannot be made without the Book of the White, a spellbook Jocelyn once owned, and that its last known location was Valentine's country manor. In the Gard, Simon shares a cell with a ragged prisoner who calls himself Samuel and who talks a great deal about the Mortal Instruments. Demons reach Alicante despite the towers, which should be impossible, and the Clave's confidence in its own defences begins to crack. Jace and Clary are alone together more than either of them can afford, with the fact of what they have been told about each other sitting between them.

Simon is got out of the Gard, and the prisoner who called himself Samuel turns out to be Hodge Starkweather, the Institute tutor who betrayed Clary and Jace to Valentine. Jace and Clary go to Valentine's abandoned country manor for the Book of the White. Following the dreams that have been troubling him, Jace finds an angel chained in the cellar beneath the house, held captive for years and unable to speak. The angel shows them both a series of visions: Valentine experimented on unborn children, giving one the blood of a demon and another the blood of an angel. Clary finds the Book of the White in the house. The angel is released and the manor comes down with him, and Jace is left with far more questions about himself than he had before.

Someone climbs Alicante's demon towers and disables the wards that keep the city safe. Max Lightwood, awake at night and quick to notice things adults do not, sees who does it, and is killed for it; his family finds him in the morning. Valentine's demons come through the failing defences in force and the city takes heavy losses. Valentine's terms are repeated to the Council: surrender the government to him, or be destroyed. Magnus has the Book of the White and can wake Jocelyn, but the Clave is in no condition to protect anyone, and the Downworlders, barred from the city and blamed for its troubles, have no reason to help.

Sebastian Verlac is exposed. He is not a Verlac at all: he is Jonathan Christopher Morgenstern, Valentine's true son, the child fed demon blood before he was born. He killed the real Sebastian Verlac and took his place, he brought down the towers, and he killed Max. He kills Hodge as well before he goes. Clary, working from what she can do that no one else can, invents a rune that binds a Shadowhunter and a Downworlder together as partners, giving each a share of the other's strengths. She takes it to the Council, and Luke brings the werewolves, vampires, warlocks and faeries to fight beside the Nephilim for the first time. Clary also marks Simon with the Mark of Cain, so that anyone who harms him suffers sevenfold. The Clave marches for Brocelind Plain.

The battle is fought by paired Shadowhunters and Downworlders, and it holds. Jace hunts down the young man who called himself Sebastian and kills him; the body goes into the river and is not recovered. Valentine takes Simon to Lake Lyn to complete the summoning, and finds he cannot spill the blood of a marked man without destroying himself, so he uses Jace instead and kills him. The lake is the third Mortal Instrument, the Mirror, and with all three Valentine calls the angel Raziel. But Clary has reached the ritual runes ahead of him and rewritten the name in them as her own. Raziel answers to her, kills Valentine, and grants her the one request the summoner is owed. She asks for Jace, and he wakes.

Magnus wakes Jocelyn with the Book of the White, and she confirms what the angel's visions implied. Jace is not her son. Valentine took him as a newborn after his true parents, Stephen and Celine Herondale, died, and raised him under a dead man's name with angel blood in him; Jocelyn's own son Jonathan, the one given demon blood, was the boy calling himself Sebastian. Clary and Jace are not related and never were. The Clave, having survived because of Downworlder help, gives the Downworlders seats on its Council and rewrites the Accords, and Alec Lightwood makes his relationship with Magnus public in front of all of them. Max Lightwood is buried in Idris. Simon returns to New York still carrying the Mark of Cain, and Jocelyn, awake at last, has her daughter back and a dead son she never speaks of easily.

Valentine's rebellion ends at Lake Lyn, which is itself the third Mortal Instrument, the Mirror. He kills Jace there and uses the summoning to call the angel Raziel, expecting to be granted command of the Nephilim. Clary has already altered the runes of the ritual so that they name her instead, so the angel is bound to her, not to him. Raziel kills Valentine and grants Clary one request, and she asks for Jace's life; Jace wakes. On the battlefield Jace has already fought and killed the young man who called himself Sebastian, whose body falls into the river and is never recovered. In Alicante, Magnus uses the Book of the White to wake Jocelyn, who confirms what the angel's visions implied: Jace is not her son and never was. Valentine took him as an infant after his true parents, Stephen and Celine Herondale, died, and raised him under a dead man's name with angel blood in him. Jocelyn's own son, Jonathan, was the one Valentine fed on demon blood, and he was the boy passing himself off as Sebastian Verlac. Clary and Jace are not related. The Downworlders who fought under Clary's Alliance rune are given seats on the Council, Alec claims Magnus publicly, Max Lightwood is dead, and Simon goes home to New York still bearing the Mark of Cain.