In November 2007, when the Clave was moving to de-prioritize the search for the missing Jace Herondale, John—acknowledging the debt and history of their families—voted to extend the search for him and Sebastian.
In December 2007, John and Cordelia were assigned to investigate some demonic disturbances near the beach caves of Leo Carrillo. They dropped Emma off at the Los Angeles Institute for training as they went. While they were away, Sebastian and his Endarkened army attacked the Institute, and Emma and the children escaped to Alicante.
While the Institute was empty, Malcolm Fade used the opportunity to steal the Black Volume of the Dead from the Institute's library. John and Cordelia arrived and ran into Malcolm, who desperately wanted to see if the dark spell from the book—which he needed to bring his beloved back from the dead—would work. Malcolm used them as sacrifices for his ritual, but their deaths were in vain as the spell failed.
Their bodies washed up in Marina del Ray and they were found stripped of their clothes, graying, and covered in the strange, ugly markings used for the ritual. Their bodies disintegrated when the Clave members tried to carry away their corpses. Supposedly given proper funeral rites, they were burned on the beach, just as the couple had previously requested. Preoccupied with the war, the Clave dismissed their deaths as mere casualties in Sebastian's campaign, killed by the Endarkened, which prompted Emma to find the real reason for their murder.
Emma spent the next five years investigating their deaths to figure out the real cause herself. After Malcolm began killing faeries and other mundanes the way Cordelia and John were killed, Emma was eventually able to discover the truth and went on to get justice, and vengeance, by killing Malcolm herself.
- John, like his ancestor Jem, played the violin.
- John liked to dance, particularly to the foxtrot. He was also a fan of jazz.