The Mortal War was a battle fought by the Shadowhunters and Downworlders of the Clave against Valentine's newly-reformed Circle and an army of demons. It took place at Brocelind Plain in September 2007.
Valentine Morgenstern had planned the whole battle with his son, Jonathan, who, in the guise of Sebastian Verlac, easily made his way into Alicante. Part of the plan involved deactivating the demon towers that protected the city in order to allow their demon allies entrance into Alicante. The towers had been engineered so that demon blood was required to deactivate them, but since only Shadowhunters can gain access to the demon towers, the towers were thought to be impossible to deactivate. Since Jonathan was exposed to demon blood while in utero, it ran in his veins along with his Shadowhunter blood, allowing him to both enter the towers and use his blood to take down the wards.
With the wards down, the fearsome army of demons that Valentine had summoned with the Mortal Sword managed to enter the city. They immediately began to lay waste to the city; fires began to spread, and their citizens were attacked so unexpectedly that even some of the Nephilim were unable to immediately fight back. And since all of the adult Shadowhunters were at a Council meeting at the Gard, only elderly Shadowhunters and those under eighteen were left to defend the city. Though the adult Shadowhunters eventually rejoined their forces, it was only because of the arrival of the Downworlders to fight alongside the Nephilim that they were able to turn the tide just enough to let the people retreat to the Accords Hall.
Despite the Clave being able to put the wards back up, there had already been many casualties in the first phase of the battle. At the Hall, Valentine, in the form of a semi-corporeal projection, gave them until midnight to decide whether they would surrender to him or fight against him.
Clary was then able to convince the Clave to fight alongside the Downworlders after she showed them a rune she "created" that would temporarily allow the two groups to share their power: the Alliance rune.
In a rush to meet Valentine's deadline, Simon insisted that Clary draw the Mark of Cain on him, in a last ditch effort to protect himself from vampires and still convince them to fight with the Nephilim and the rest of the Downworlders, as the vampires were the only ones who had decided to sit out. Raphael agreed to fight with them in exchange for Simon, not realizing that he would be unable to harm him, thanks to Simon's Mark. Being a man of his word, he and his clan were left with no choice but to participate in the war, though Raphael demanded that Simon fight with them to compensate for tricking him.
Against his father's instructions, Sebastian impulsively sent out the demons into the city before midnight, in an effort to hurt and scare Jace.
Behind the action, a different conflict was taking place. Jace, later aided by Isabelle, faced off against and killed Sebastian. It was also during this brief confrontation that Jace learned the truth about his lineage.
Jace then went to Lake Lyn to confront Valentine, who was about to kill Clary to use her blood to summon the Angel Raziel. Jace confronted Valentine about his lies and was killed by him shortly after; Valentine used Jace's blood, instead, in the summoning ritual.
Valentine then proceeded to summon Raziel, though unbeknownst to him, Clary had changed the runes in his summoning ritual to represent her as the master of the summoning circle—of Raziel's granted wish—instead of Valentine. Once Raziel appeared to them, he was furious that Valentine had summoned him, as a Shadowhunter with such ill will for his kind. Enraged at his actions, Raziel struck Valentine down, and granted Clary her one favor, one she had no difficulty choosing: the resurrection of Jace.
Unfortunately, Jace's resurrection was an incident that caused an imbalance in nature which would ultimately lead to more problems, especially because the event was witnessed by Lilith from afar, who knew she would be able to use the imbalance to bring back her "son," which ultimately led to the next war.
Meanwhile, the battle against demons in Alicante was won within minutes, thanks to the Alliance rune and the newly found effectiveness of the partnership of Downworlders and Shadowhunters. Despite the many casualties, most of whom were given Shadowhunter funerals, including Valentine, a celebration was held to commemorate their victory and the formation of the New Council that included seats for a representative of each Downworlder species, a gesture of the Clave's appreciation of their help during the Mortal War.