After the Dark War, during which Jon was not in Alicante to participate in the battle for some reason, Jon was among the many young Shadowhunters who decided to attend the newly-reopened Academy in Idris. There, he met and briefly befriended famous mundane Simon Lewis. He claimed to be friends with Jace Herondale, boasting that he taught Jace a couple of things. He and Julie made several snide remarks about the mundane class, insultingly calling them "dregs", and Downworlders, finally pissing off Simon. Because of them, Simon moved to be trained with the mundane stream, instead of under the Shadowhunter "elite" curriculum.
During the course of their two years at the Academy, Jon and the other Shadowhunter students came to see some of the mundane students as friends. Jon, Beatriz, and Julie all became close to the mundane aspirants Simon, George, and Marisol. Sometime during their second year, Jon briefly dated Julie. He also grew particularly close to Marisol, who started out with annoying him about mundane contraptions. Unbeknownst to him, George and Simon named all the rats they found in their rooms after him—though this was, much later, all in good fun.
In 2012, Jon was sent to the Los Angeles Institute as part of a Centurion team to search for Malcolm Fade's body and the Black Volume of the Dead. He participated in patrols with the Centurions and remained friendly with the residents of the Institute during their stay. Along with a number of other Centurions and the residents however, they were forced to put up with Zara Dearborn's rants about Downworlders. Once, he stormed off—presumed by Kit to be because of an argument with Zara—and came across Malcolm's reanimated body along with his small army of sea demons and was killed. Malcolm took his severed head and showed it to the Blackthorns and the others when he revealed himself to them. His death greatly upset Marisol.
Jon was burly, with arms apparently the size of Simon's head. Jon also had a thick neck, which made Magnus easily deduce that he was a Cartwright because all of the Cartwrights he has met over the centuries had thick necks.