Even before the series was cancelled, Freeform planned to air "Shadowhunters" Season 3 in two parts, meaning the final ten episodes weren't filmed yet when the news came out. In order to make story adjustments and write the two-part finale, the second half of Season 3 was pushed back and didn't premiere until a year after Season 3's first episode aired.
In the two-part finale, Clary, her boyfriend and fellow Shadowhunter Jace (Dominic Sherwood), Shadowhunter siblings Alec (Matthew Daddario) and Isabelle (Emeraude Toubia), and Simon must all work together to rescue the warlock Magnus (Harry Shum Jr.) — who is also Alec's fiancé — from the demon realm called Edom. While there, they also must stop Clary's half-demon brother Jonathan (Luke Baines), who is working with evil forces to destroy the Shadow World. Clary knows that she is the only one who can stop him, and so even with the possibility that she might lose her life as a Shadowhunter if she goes after Jonathan, Clary does it anyway, destroying her brother and saving the Shadow World.
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. In the final scene of "Shadowhunters," Clary is at an art show, having finally become the painter she always dreamed of being, when she spots a handsome young man with strange tattoos on his neck — Jace. Could this be her reintroduction to the world of Shadowhunters? Well, it's up to your interpretation.