2(Shadowhunters)

An Au where Asmodeus steals Jonathan before Lilith gets to do anything to him and brings him to Magnus? Like, he wants to be the only ruler of Edom and with Jonathan having Lilith's blood on him it would make him his competition.

Wouldn't make more sense for Asmodeus to kill Jonathan? Maybe but perhaps he thought that by giving the child to Magnus his son would agree to help him when he wished for it.

Magnus immediately realizes that Jonathan is Valentine's son but even then he decides to raise him as his own both because the children shouldn't pay for the parents sins and because Jonathan's powers could ge out of control and hurt himself and others if he wasn't taught as it should be.

Jonathan Morgensten becomes Jonathan Bane and his raised in secret by Magnus who believes doing that is safer so no one tries to get revenge on Jonathan for what his father did and for no Circle member to find his child and try to use him to further their plans.

When Jocelyn runs away, she never approaches Magnus for anything as Dot talks with some warlocks and they decide it is for the best to make Jocelyn believe Clary is her goddaughter/niece then the truth to help protect the girl better from her father and the Circle members(Luke would teach Clary how to be a shadowhunter without revealing that to her until she was about 16/17 where they would reveal the truth to her...if they reveal her true parentage is up to the writer)

Thanks to that, warlocks and others(werewolves and vampires) decide to keep an eye on the children of other Circle members' children as if they had been as they did then who says they would be good parents to their children and not try to use them for Circle plans ro to absolve their crimes.

Every children from Circle members end up having an aunt/uncle, who they never inform their parents about, who protects and teach them that the world isn't fully black and white.

Camille still attacks Simon but it is before Clary's birthday and he is saved by Raphael who takes him to Magnus to be protected as Camille may try to turn him latter so Jonathan gains a friend in Simon.

How would the first meeting between Alec and Magnus go? Maybe similar to canon or Tessa(who would be the keeping an eye on the Lightwood siblings, especially Jace who looks like an Herondale instead of a Wayland) tells Alec that if something happen and they can't contact her to go to Magnus and they do it(what happened for them to need Tessa/Magnus? Maybe one of them was hurt by a demon and the injury isn't healing like it should? I have no idea).

Would Jonathan being Magnus' son affect his relationship with Alec? Maybe in the terms that it makes more obvious that Magnus has been alive for longer or when it is found out Jonathan's true parentage and how he came to be in Magnus' care but otherwise I don't think it would affect too much.

Would Clary join the New York Institute? Yes, after Luke and Dot tell her the truth she decides that she wants to be a shadowhunter especially as she believes being one will help her find Simon who had disappeared a month or so before her birthday.

Anything else is up to the writer but there needs to be a reaction of the Circle members finding out that their children have been partially raised by downworlders who said children trust more then their own parents.

Also, if you decide to have Asmodeus approach Magnus again it would be to request for help to finally kill Lilith(or maybe when he went to give him Jonathan they made a deal were Magnus would help his father when the time to kill Lilith comes).