Clary Fray, is a Shadowhunter who was raised among normal people (a.k.a. mundanes), robbed of her memories of true ancestry. When her mother was kidnapped, Clary's simple life was turned upside down as she was forced into a journey of self-discovery in a dark world of demons and other creatures.
Clary is the second child of Jocelyn Fairchild and Valentine Morgenstern She was born after her brother, Jonathan Christopher Morgenstern whom most everyone believed perished in a fire with her father. Her mother and father, both Shadowhunters, belonged to an extremist organization of Shadowhunters called the Circle.
Before she was born, her mother went fled to New York, leaving her life as a Shadowhunter behind. While playing at a park when she was young, Clary was almost attacked by a demon but was saved by her mother. After the incident, Jocelyn rushed her to Magnus Bane, a warlock, and begged him wipe the memories of the Shadow World from her mind. For years, Jocelyn led Clary to believe that her father was a man named Jonathan Clark.
Throughout Shadowhunters: The Mortal Instruments
Clary started her 18th birthday with an interview at the Brooklyn Academy of Art. Clary was accepted into the advanced program she'd applied for, and said that the graphic novel sketches that were in here portfolio by accident is what really caught the panel's attention.
She met Simon Lewis, her best friend, for coffee were she pretended to be upset then gave him the good news about get into the program. After meeting with Simon,she went home to give Dot and her mother the good news. After hearing the news, Jocelyn gave Clary a gift that she called a family heirloom and tried to have a serious conversation with her. Clary brushed her off and went got ready to go to Simon's bands, called the Champagne Enema at the time, gig. Luke, a good friend of Jocelyn and a father figure to Clary, stopped by to give Clary a gift of spray paint and again tried to have a serious conversation with her, which Clary again brushed off.
Later that evening outside of Pandemonium Club, Clary encountered Jace Wayland when he bummed her shoulder, she had a brief conversation with him when he asked "You can see me?" After the conversation, she talked to Simon and about it, they both stated that their was nobody there. In the club she follows the guy that had bummed in to her outside and sees him and two others fighting with what looked like monsters to her, at one point picking up a dropped sword and killing one of the monsters when it was thrown in to it. Freaked out by the battle she witnessed at the club, she rushed out of the club, bumping in to Magnus Bane, whom she has a vague, confusing flash of memory about. At home, Clary told Jocelyn about what had happened. Jocelyn started to tell her that she was a Shadowhunter when a group of men arrived, scaring both Jocelyn and Dot. Jocelyn wrapped a necklace around her neck and sent her into a Portal that took her to the NYPD station, to Luke.
While at the station, however, she overheard a conversation between Luke and two people about how he cares nothing for the Frays. Believing what she had over heard, she rushed back home to find Jocelyn missing, and a demon that had shapeshifted into Dot attacked her. Jace, one of the Shadowhunters from the club, arrived just in time to save her life, but not before she is scratched/bitten by the demon. Clary collapsed from the demon venom, and he carried her back to the New York Institute to recuperate.
Upon waking, she met Isabelle and Alec Lightwood. Jace begins to tell her of the basics: that they, including her, were all Shadowhunters, human/angel hybrids, whose duty was to protect the human world from the shadow world, and that vampires, werewolves, demons, all the stories are true. After finding out that she was a Shadowhunter, Hodge Starkweather, the Institute's trainer and former Circle member, told her that her mother was once part of the Circle—the organization, led by Valentine Morgenstern, that abducted her.
Up on discovering that the Circle was search for The Mortal Cup, Clary works along side the Institute to find the Cup and her mother.
In hopes to unblocked her lost memories, the Shadowhunters brought her to the City of Bones, where the Silent Brothers used the Soul-Sword on her. Even though none of her memories were able to be retrieved, the Silent Bothers were able to discover that she was in fact the daughter of Valentine Morgenstern. Clary compels the others to save Simon when he is kidnapped by vampires and held at their den, the Hotel Dumort. A vampire named Raphael who did not agree with Camille, the vampire that abducted Simon, and a pack of werewolves help them and they were able to escape with Simon.
Believing that her lost memories will aide in finding the Cup, Clary told them of a fuzzy memory from her youth where she saw a man named Magnus taking her memories. Simon told them that Camille had told him about Magnus Bane when he mentioned Clary's missing memories.
The group lured Magnus out of hiding with a party, and while the warlock initially refused to help them, he eventually agreed when they helped him fight off Circle members that attacked his safe haven. To her surprise, Magnus also told her that Dot was tortured and killed by Valentine. Magnus then told them that he fed Clary's memories to a memory demon, Valak, for safekeeping. They decided to summon the demon, Clary drawing the elaborate pentagram for summoning him on the floor, but when Jace's life was put at risk, Clary decided to sacrifice her memories and banished the demon to save him.
Even without her memories, Clary was eventually able to find the Cup by pulling it from one of Dots tarot cards. While Valentine posed as Michael Wayland, Clary caught onto his deception and gave him the fake Cup, after which Valentine revealed to them that she and Jace were siblings—that he was Jonathan, and was his son with Jocelyn. They were able to rescue Jocelyn from Valentine, although she was still asleep under the potion she took, Clary began searching for the Book of the White that contained a spell that could wake her mother.
The Cup was lost when Hodge betrayed them and gave the Cup to Valentine. After they found the book and were able to revive Jocelyn, Jace felt he had no choice but to join Valentine.
As a Shadowhunter
The reunion with her mother was short lived as Clary soon became preoccupied with their troubles. She broke the news to Jocelyn that Jonathan was alive and was taken by Valentine, not knowing that Jocelyn felt that Jonathan was innately evil and would later try to kill him. Along with this, she was closely watched by the new head of the Institute's, Victor Aldertree.
Alec blamed Clary for everything that was going wrong, making her start to doubt her sense of belonging—unable to fit in among the Shadowhunters and also unable to return to her former mundane life. In an attempt to feel herself again, she went to the Brooklyn Academy of Art to paint. Jocelyn and Luke, concerned for her safety, came to her in an effort to convince her to return to the Institute but she was distracted when she saw Dot who then took her through a portal to Valentine's ship. Clary mind-controlled by Dot to trick Jace into submitting to Valentine. Clary was able to get through to Dot, who then later helped her and Jace escape the ship by taking down the wards with her magic.