When the Uprising came and Jocelyn was able to steal the Cup from Valentine, they ran, but without Clary's older brother as Valentine had made it look like the child died in a fire with him.
Jocelyn wasn't confident about Valentine's death however, suspecting that he was only in hiding, and fled to Paris, and later New York City; ran from the Shadowhunter world and culture, away from her past, and raised Clary as a mundane.
With Jocelyn worried about Clary's Sight and potentially running into elements of the Shadow World, she informed Clary the following morning that they were going to spend the summer at Luke's farmhouse, infuriating Clary who had her own plans, including her ongoing Tisch classes.
Clary left with Simon without hearing Jocelyn's reasons.
Tessa stood in for the Iron Sister, and for the needed Silent Brother, they were able to call on Brother Zachariah.
Clary and Jocelyn then took the surname "Fray"—a portmanteau of Fairchild and Gray, chosen as gratitude for Tessa, to honor the her relationship with her ancestors.
During the time after Jonathan's birth, Jocelyn suffered depression because of her strange feelings of rejection towards him.
Hoping to help Jocelyn, Valentine secretly gave her doses of the angel Ithuriel's blood, hoping to "cure" her depression, unaware that she was pregnant with Clary, therefore making her an "accidental" experiment.Jocelyn's best friend Luke eventually found them in New York, and Jocelyn allowed him to be a staple part of their lives. she met Simon Lewis and the two grew to be inseparable.Clary grew up with Luke as a father figure to her, led to believe that her real father was a deceased soldier named Jonathan Clark, and that the box in her mother's room with the initials J. Almost every summer of her childhood, she, Jocelyn, Luke, and Simon went to Luke's farmhouse upstate.Clary was unknowingly supposed to have another session with Magnus in 2007, two years after the last.Magnus had gone to Tanzania, however, so Clary went without her block for at least three weeks, and thus her Sight began to return.Jocelyn asked Magnus to remove her Inner Eye, but this would have put her at risk, so they compromised with a spell that placed a block on her mind that would make her forget what she saw of the Shadow World even as she saw it, but the spell was complicated and needed to be recast every two years.