He is also the main antagonist of the dark/fantasy Freeform 2016 television series Shadowhunters: The Mortal Instruments, initially starting off as a background antagonist in the first season and a flashback/unseen antagonist in Season 2A. He later gains a more pivotal role as the secondary antagonist in Season 2B, a posthumous antagonist in Season 3A and the main antagonist in Season 3B.
He was played by Will Tudor disguised as Sebastian Verlac in Season 2B and two episodes of Season 3A. Elias Toufexis played his true, charred form in two episodes of 2B. For Season 3B, the role was recast and Luke Baines played his true restored form.
Before he was born his father Valentine fed Jocelyn demon blood from Lilith, a Greater Demon. This caused Jonathan to be born with dark eyes and have no good in him. Sometime later Valentine faked his and Jonathan's deaths and went into hiding and started training his son to become the ideal spy while also raising Jace Herondale.
Years later Jonathan went to Idris under the name of Sebastian Verlac (the real one he killed) in order to put down the wards to let demons in. He succeeded this and ended up killing Jace's adoptive brother Max as he saw him do it. He is later killed by Jace.
However Lilith found his body and was determined to revive him and forced Simon Lewis a Daylighter Vampire to bite him and give him blood but this process was only half complete as Simon was able to get rid of Lilith by using the Mark of Cane. But later Jace was tricked into applying a rune which bounds him to Sebastian. But Clary was able to server the bound by stabbing Jace with a sword called Glorious.
Jonathan now deciding to keep the name Sebastian then later used the Infernal Cup to create Endarkend Shadowhunters to fight normal ones and Downworlders. He also wished to rule Hell with Clary by his side.
In the final book City of Heavenly Fire he is fatally wounded by Clary who stabs him with one of the Morgenstern family swords Heosphoros (which was filled with heavenly fire) which destroys the demon blood in Sebastian's body and becomes good and asks to be called Jonathan. But there is not enough good in him for him to survive and dies in his mother's arms after apologising for his actions as Sebastian and is later cremated.
Jonathan/Sebastian had blond hair (like his father Valentine) which he briefly dyed black whilst undercover and had black eyes (due to the demon blood). But after becoming good, his eyes turn green (which would have been his natural color if he hadn't had demon blood in him).
- Jocelyn Fairchild - Mother
- Valentine Morgenstern † - Father and Former Attempted Victim
- Lilith † - Adoptive Mother and Attempted Victim
- Clary Fairchild - Sister, Attempted Victim and Killer
- Lydia Branwell (TV series) - Distant Relative
- Henry Branwell - Distant Relative
- Charlotte Branwell - Distant Relative
- Rachel Branwell - Distant Relative
- Matthew Fairchild - Distant Relative
- Charles Buford Fairchild - Distant Relative
- Jace Herondale - Adoptive Brother, Kidnappee, Attempted Victim
- Ash Morgernstern - Son
- Jace Herondale - Attempted Victim
- Clary Fray - Attempted Victim, Killer, Kidnappee
- Isabelle Lightwood - Attempted Killer, Attempted Victim
- Alec Lightwood
- Magnus Bane
- Luke Garroway
- Jocelyn Fairchild
- Simon Lewis - Attempted Killer
- Max Lightwood (Book) † - Victim
- Max Lightwood (TV Series) - Attempted Victim
- Maryse Lightwood
- Robert Lightwood
- Sebastian Verlac † - Kidnappee, Victim
- Aline Penhallow
- Dot Rollins - Attempted Victim
- Raphael Santiago - Victim
- Raphael Santiago (TV Series)
- Duncan † - Blackmailee and Victim
- Cleophas Graymark
- Elliot Nourse †
- Seelie Queen - Former Lover
- Mirek † - Victim
- French Shadowhunter † - Victim
- Lanaia † - Temporary Servant turned Enemy and Attempted Killer
- The Clave
- Jonathan is similar to Luke Castellan as both have blonde hair, both are related to the protagonist (Jonathan is Clary's brother whilst Luke is Percy Jackson's first cousin once removed). Both also are killed by blades (Luke stabbed himself in his Achilles Heel with Annabeth Chase's Celestial Bronze knife to destroy Kronos who was using his body as a vessel and died soon after, whilst Jonathan was stabbed by Clary with Heosphoros filled with heavenly fire) and make peace with the protagonist before they die.
- Jonathan has a son with the Seelie Queen, who is currently around 13 years old. His name is Ash Morgenstern.