One evening in August 2007, Clary, Simon, and the band came to the café for the poetry reading to support their participating friend Eric. It was also then and there, specifically in the back alley, that Clary and Jace saw and spoke to each other again after their first encounter at the Pandemonium Club.
In May 2008, an amnesiac Simon went to Java Jones. While Asmodeus managed to wipe the memories of the people close to Simon, making them forget about Clary and Simon's absence, the barista at the café was among those minor connections of the pair that was left untouched by the curse. When Simon came in alone, she inquired about Clary, referring to her as the pretty girl Simon always came there with and ordered her coffee black. Since Simon did not remember Clary, he told her that she must have mistaken him for someone else, leaving the barista confused.