The Dark War was a great battle against Sebastian Morgenstern and his army of demons and Endarkened Shadowhunters. The war was at its height during the battles fought in December 2007: one in Alicante, and another in Edom.
Sebastian, with the help of Lilith, was revived after being killed by Jace Herondale during the Mortal War. Upon his resurrection, Sebastian was also able to bind himself with Jace through a demonic twinning spell, with Sebastian as the superior of the pair. With Jace and a deceptive Clary at his side, Sebastian began his plans in Prague. With Sister Magdalena, Sebastian had the Infernal Cup made, an idea Jace had given him. He also worked with demons and, eventually, resurrected his "mother" Lilith, after Simon Lewis momentarily destroyed her and scattered her essence in the Void.
Infusing the Cup with his and Lilith's blood, Sebastian made the remaining loyal followers of Valentine Morgenstern, and those unhappy with the Clave, as well as the kidnapped Amatis Herondale, into Dark Shadowhunters with a ceremony at the Seventh Sacred Site in the Burren. With this, Sebastian had around forty to fifty men in his army, all of them blindingly loyal to him. However, Sebastian lost both Jace and Clary before he could turn either of them into Endarkened after he was confronted by a group of Shadowhunters and Downworlders who came to rescue them. Shocked at the sudden severance of his bond with Jace, and the defeat of most of his Endarkened army, he retreated.
Sebastian made an alliance with the Seelie Queen, a partnership that few were aware of, enabling the faeries to get information from the Nephilim without suspicion. The queen allowed him to use her faeries to help him in his endeavors, providing them with protection, faerie warriors, access to ley lines, and a means to strengthen their numbers, aiding Sebastian in making his army grow by launching a series of onslaughts on several Institutes around the world, forcibly turning the Nephilim they capture into Endarkened. They struck the Institutes in Bangkok, Buenos Aires, Oslo, Berlin, Moscow, and, Los Angeles in quick succession, before the attacks could be reported and warnings could be passed around. Every Conclave in these cities had its Shadowhunters captured and Turned, while the ones who would be unable to fight were killed.
The attack on Los Angeles was the first to yield the first survivors of the attacks. They were able to send along the message not only of his attack, but that Sebastian was nearly invincible thanks to Lilith. The Institutes around the world were immediately alerted and ordered to evacuate to Alicante. Sebastian then attempted to attack the London Institute, though a force protecting it thwarted his attack.
After the failed attack on the London Institute, Sebastian turned his attention to the Praetor Lupus in New York City. He burned down the building and massacred all the werewolves there. Before leaving, he stabbed Jordan Kyle in front of Maia Roberts to pass on a message to the rest of the Downworlders: if they allied themselves with the Nephilim, they would meet the same fate.
Sebastian later attacked the Adamant Citadel as a ploy to drive out the Shadowhunters as a distraction from his true goal, to capture Jace and Clary. It was also a learning experience to see how well the Clave could battle the force of his army. When he stabbed Jace, he was burned by heavenly fire, showing that he could still be harmed by something. He and his forces promptly fled.
Days later, he snuck into Alicante and paid Clary a visit. While succeeding in terrifying her, that was not his only objective. His reason for the visit was to kidnap the Downworlder representatives. Meliorn, in cahoots with Sebastian, spiked their wine at dinner so that they would all be rendered unconscious. At the Council meeting the next morning, their absence was noted upon Sebastian's message on the floor: Veni—I have come. During the meeting an Endarkened seized Jia Penhallow, threatening to slit her throat. He then announced that in order for the return of their Downworlder representatives, they must surrender Jace and Clary to him. He also offered them survival: they could live should they agree to either drink from the Infernal Cup and become Endarkended or stay as Raziel's children locked in Idris, never to leave, granting Sebastian the rest of the world. He gave them two days to decide before vanishing.
Prior to the deadline, Sebastian appeared to Jia for her answer. Though at first she countered his question saying it was too early, the Council had decided against giving him Jace and Clary. He simply laughed, knowing that Clary and Jace, along with their friends, had already left and were on their way to him. Later, after confirming their departure, Jia received word from Mark Blackthorn—who had been taken by Sebastian and was now a member of the Wild Hunt—that the Fair Folk were working with Sebastian and were their enemies. This information was especially useful when they later received a missive from Maia telling them of Sebastian's plans to attack Alicante. They were not only able to prepare for the oncoming battle by hiding the children and making sure everyone was armed and ready for a fight, but they were also able to Faerie-proof the city with help from the Spiral Labyrinth.
While Sebastian's forces invaded Alicante, Clary, Jace, Isabelle, Alec, and Simon invaded Sebastian's base in Edom. Having previously discovered that Sebastian could be harmed by heavenly fire, Clary had managed to remove the fire from Jace's veins and into her blade with a rune she created. While her friends split up to find and rescue his hostages, Clary faced down Sebastian and seemingly agreed to his offering of her ruling beside him in exchange for the end of his attacks on their world. When he asked for a kiss to seal the deal in front of everyone, she took advantage and stabbed him through with her sword. The heavenly fire burned all that which was evil in him, leaving only the minor shell of who Jonathan could have been. As there was not enough good to survive the fire, he quickly told Jace where the cup was and how to destroy it before succumbing to death. Upon doing so, all the Endarkened, both in Edom and Alicante, died. Seeing their fallen partners, the faeries in Alicante fled and the war was won.
- Praetor Scott - killed by Sebastian Morgenstern
- Numerous Praetor House residents - killed by Sebastian Morgenstern
- Jordan Kyle - stabbed through the chest by Sebastian Morgenstern
- Meliorn - shot in the chest with an arrow by Alec Lightwood
- Maureen Brown - decayed to ashes when Maia Roberts tricked her into biting her but she had previously injected herself with holy water which is fatal to vampires
- Raphael Santiago - stabbed through the heart by Sebastian Morgenstern
- Sebastian Morgenstern - stabbed by Clary Fairchild using her heavenly fire-infused sword Heosphoros
- Amalric Kriegsmesser (Endarkened) - died after attempts to cure him failed
- Andrew Blackthorn (Endarkened) - killed by his son Julian who threw his short sword into his chest
- Elizabeth Beauvale - killed by a faerie in the battle at Alicante
- Tomas Rosales - killed in the battle at Alicante
- All Endarkened warriors - killed when the Infernal Cup was destroyed
- Several fey warriors - killed in the battle at Alicante
- Several Shadowhunters - killed in the battle at Alicante
After the war was over, the Shadowhunters became desperate to make their enemies pay for their sins. The faeries were subsequently forced to accept their severe terms, else be thrust into a war against the Shadowhunters. The terms included the disbanding of their armies and a weapon ban among their kind, a huge blow to the Fair Folk who are known to be warriors and needed weapons to defend themselves. There were other terms, still being straightened out by the end of 2007, but the faeries were also made to take responsibility and pay for the losses and damages done to the Nephilim and the Downworlders, such as the rebuilding of the wards and Alicante, as well as the reestablishment of the Praetor Lupus. In addition to this, half-faeries Mark and Helen Blackthorn were both punished; Mark was left at the mercy of the Wild Hunt, while Helen was exiled to Wrangel Island. This treaty between the Shadowhunters and the fey would become known as the Cold Peace.