This is actually a really big part of the plot in the first three books. At the end of City of Bones, Valentine Morgenstern, reveals to Clary and Jace that they are siblings, and his children. Jace is not Jonathan Christoper Wayland, as he believed, but Jonathan Christoper Morgenstern.
Jace's legal name changes throughout the series, from Jace Wayland (when his father is thought to be Michael Wayland), to Jonathan Morgenstern (when thought to be Valentine's son), to Jace Lightwood for the family that has taken him in, to Jace Herondale (when his true father is revealed to be Stephen Herondale).
It isn't until the last half of the third book, City of Glass, do we learn that the two aren't related at all. However, in the movie, to appeal to a larger audience it was safer for the viewer to be in on the secret.
In book three, Jace and Clary find out that they aren't actually siblings. Phew! But after more looking into the spoilers I found out that Jace and Clary kiss a few more times while they still believe they are siblings.
At the same time, Valentine continued trying to get Jace to embrace his beliefs. He told Jace that he had demon blood in him and tried to convince him that, because of the demon blood, he had an inclination to kill and would always want his "sister" the way he can't have her.
Clare is sharing the original draft version of the scene where Jace kisses Alec to reassure him about Magnus: “Drop it, Jace,” Alec said in a warning tone. Jace was having none of being warned. “Magnus says it's because you're hung up on me.
Lilith noted his kindness and chose him as her first disciple. At one point, she managed to call for Jace. She put him under her control, turning him into a loyal foot-soldier by having him possessed with her demonic Owl, but only able to do so in his sleep because of his strong love for Clary Fairchild.
Clary and Jace spent the novel on some mission in Faerie. They're still together, but Clary turned down Jace's proposal of marriage. She did so because believes that she is going to die soon. She's okay with it, though.
Despite the success of her mission, Clary is turned into a human and forced out of the Shadow World, with her memories of the last few years with Jace and the others gone.
Sacrifice has always been a major theme on this show, so it made sense for Clary to have to give up what she loved most in order to fulfill her destiny. The fact that she and Jace still ended up together in spite of that was a welcome treat that I wasn't expecting.
They even thought they were brother and sister at one point in the series… Still, through every trial and every loss, Clary and Jace's love stood strong. Their feelings would never falter no matter what fate had in store.
Shadowhunters: Clary Learns Jace Is Not Her Brother In Ep. 11 — Recap – Hollywood Life.
It seems the real reason why City of Ashes never happened is that they couldn't find a way to make the book series work as movies. "It actually makes sense to do [the novels] as a TV series," Moszkowicz told The Hollywood Reporter.
Valentine wants it so he can create a new race of Shadowhunters. That's why Jace and Clary needed to find the moral cup, to stop Valentine from creating new Shadowhunters that would kill people who don't survive the process.
While Valentine took the identity of Michael Wayland, Jace was raised as Jonathan Wayland, both of whom were, in fact, the father-and-son Valentine killed to fake their deaths. Jace was raised by Valentine believing that they were the Waylands, and they lived in the Waylands' estate.
Clary had been having ominous dreams of her death and feared leaving him in pain. When she eventually realized that the death she was seeing wasn't hers but was in fact of an alternate version of hers, Clary herself proposed to Jace, after surviving another war and this time during Alec and Magnus's wedding.
Lilith threatens Simon with Jace cutting Clary's throat if he does not provide her with his blood, and when he doesn't, Jace cuts Clary a little. With a start, Clary realizes that Lilith is the very demon who provided Valentine with her blood to experiment on Sebastian. Clary is forced to tell Simon about Jace's death.
After disobeying the Angel's orders, Clary was stripped of her runes and was thought to have been transformed into a mundane. However, Clary is still a Shadowhunter as she was able to see Jace even though he was glamoured revealing that she still has her powers.
To add insult to injury, The Clave found out Clary used their one wish to resurrect Jace, and while she argued her case well, they still decided to execute her for her crimes. Her friends better bust her out of Alicante before her sentence is carried out, or this is going to be one seriously bloody midseason finale!
Eventually, he admitted his feelings to Clary, and they became a couple. They later realized Clary was still in love with Jace, and they were better off as friends. Even though Simon was heart broken, he and Clary promised each other to stay each other's best friend and that's what they've done.
Shadowhunters Season 3 Episode 5: Lillith Erases Jace's Love for Clary - TV Guide.
Rouse will force Clary to be impregnated by a demon, to give birth to a warlock — a dying breed. Dr. Rouse has an elixir that makes it possible for Shadowhunters to get pregnant by demons, and Clary realizes that Dr. Rouse had spiked her tea.
However, Lilith reveals that she gave Blackwood the Mark of Cain before he left, which means no one can hurt him. And in exchange, he gave Lilith the Dark Lord's seed. She is pregnant with his child.
Lilith is a principal character in Stephen Brust's To Reign in Hell (1984), where she is the love interest of both Satan and Lucifer at varying points.
Magnus had obtained enough power and used it on him to release Jace from his mental prison. Jace and the Owl fought for control of his body. Jace won and the Owl's essence was expelled from his body through his mouth in the form of black blood, and the blood sizzled, leaving no physical trace of the Owl demon.