Jonathan Sims is the current Head Archivist of the Magnus Institute, London. His predecessor was Gertrude Robinson, who passed away in March 2015. He is a seemingly rude and short-tempered man, being dismissive and condescending towards written statement givers and especially towards his assistant Martin Blackwood.
Jon is canonically asexual as confirmed by the creators in the third season Q&A, though it has been hinted at in the podcast.
For all his attitude, Jon isn't a brave man. He shies away from violence and panics if threatened, stutters if intimidated or scared. He doesn't have much courage, but is very persistent. He's self-admittedly scared of the monsters and supernatural subjects of statements, but covers it up with a scornful exterior. Jon is genuine and sympathetic to the statement givers who have come to the Institute in person and have been traumatized or scared by what they experienced in their statement.
Jon has never been described physically. The only visualizers given are that he looks like he hasn't slept in a week, has premature greying hair, and worm scars from the events of MAG 39. It can be inferred that one of his hands has burn scars from MAG 89, and that he has scars from various other encounters.
Several different characters have called him 'little,' but it's unclear if this is in reference to his stature or a condescending insult. Additionally, in MAG 79 Jon comments that the pipe he's been carrying is useless for defense, as he's getting tired just by holding it. Jon could be physically smaller or just weaker than Elias, who had no trouble using it.
Jon was a smart but difficult child. He got bored easily and would wander off. His grandmother found books were helpful for keeping him in one place, but he hated to read anything he felt like he'd already read before, meaning most authors could only provide him one book.
His first experience with the supernatural occurred when he was 8 years old, around 1995/96 – an early encounter with a Web-related Leitner book that claimed the life of an 18 year old that bullied him. He has had a dislike of spiders ever since.
He took a job with the Magnus Institute's research department in 2011, four years before being made Head Archivist in 2015.
Jon starts out cranky at Gertrude and dismissive of many of the cases, believing that reports of the truly arcane or esoteric are few and far between, though events of late are starting to seem worrisome. He has done almost all of the audio recordings for the Magnus Archives. He is helped by archival researchers Martin Blackwood, Sasha James, and Tim Stoker, though he seems to hold Martin in particularly low regard, at least until after the latter’s encounter with Jane Prentiss. Jonathan Sims is keen to digitize the Archives; however, attempts to record certain cases onto his laptop have caused significant audio distortions, so he has had to settle for recording onto archaic tape recorder.
Following Martin's encounter with Jane Prentiss and her subsequent siege of the Institute, he has become more and more concerned about the dangers of his job, including a sense that he and his co-workers are being hunted.
Jon survives the Prentiss attack with worm scars and significant mental trauma, stalking and mistrusting his assistants.
After the attack on the Archives, Jon is forced to take a month off to recover. His paranoia builds after the reveal of his murdered predecessor, and Jon becomes suspicious of all the Archive employees. He starts keeping two tape recorders - a normal one, and second supplemental to record his suspicions. Martin notices Jon's agitated behavior, and gives him a jar of Jane Prentiss' ashes in an attempt to assuage him.
During some of his time off, he sneaks into work at night to explore the tunnels under the Institute. In MAG 41 he chronicles his explorations, finding evidence of someone living in the tunnels, but eventually pauses exploring after a harrowing encounter in one of the lower levels.
Jon seems genuinely baffled at Martin's worry for him. He even goes so far as classifying his behavior as suspicious, wondering if Martin is trying to hide something from him by making Jon take time off.
Jon stalks his assistants at their homes and spends a significant amount of time after work exploring the tunnels. He gets Basira Hussain to bring him tapes recorded by Gertrude from her murder investigation.
Jon eventually takes an axe to the table held in artefact storage, which leads to him fleeing supernatural terrors. He is then rescued by Jurgen Leitner, who tells him about the existence of The Entities before being brutally murdered by Elias Bouchard.
Wanted for Leitner's murder, Jon hides out at Georgie's house and gets Melanie to find info for him from the Archives while he's on the run.
He goes to Jude Perry and Michael Crew for statements. As Michael Crew finishes his, Alice "Daisy" Tonner knocks on the door and tries to kill Jon. Basira saves him, and they go interrogate Elias about Gertrude's murder.
Jon and Daisy later capture and interrogate Sarah Baldwin about The Unknowing, which gets the attention of Nikola Orsinov, who first tries to get him to find the ancient skin Gertrude stole, but later just kidnaps him, intending to use his skin for the ritual herself. Michael shows up to kill him before she can, but is replaced by Helen, who decides to rescue Jon instead.
Jon travels to China and America. In the latter, he meets Trevor Herbert and Julia Montauk. He talks to Gerard Keay in the Skin Book and learns about the entities in greater detail. After being away from the insttitue for weeks, he finds out he has a "physical dependence" to statements, ending up sick if he goes too long without them.
Jon stops The Unknowing with the help of his assistants but ends up in a coma.
Jon wakes up from his six month coma after a visit from Oliver Banks and subsequently starts referring to himself as "The Archivist," marking his acceptance of his powers and the Beholding.
After he gets out of the hospital, he resumes his position in the Archives and comes back to find Melanie and Basira have moved into the Institute as it's too unsafe outside, Tim is dead, Daisy is missing, and Martin is absent. He's worried about Martin working with Peter Lukas, but stays away from Martin after he asks Jon to leave him alone.
Jon finds out Daisy is still alive - trapped in the coffin. Breekon breaks into the archives meaning to attack Jon, but ends up fleeing after Jon forcibly extracts a statement from his mind. The coffin is left behind. Jon discovers he could go into the coffin and have a chance of coming back if he has a physical anchor - a body part - left behind to come back to. After attempting to chop off a finger for an anchor and having his super healing deny him, Melanie takes Jon to Jared Hopworth the Boneturner, who is trapped in Helen's door after his attack on the Archives. In return for his freedom, Jared agrees to take one of Jon's ribs out. Jon offers another rib to Jared for his statement. He goes into the coffin and finds Daisy, but is stuck inside with her. They only escape when Jon is guided back by the dozens of tape recorders replaying statements on top of the coffin. The tape recorders are later revealed to be left there by a worried Martin.
Jon and Basira travel to Ny-Ålesund to stop what they assume is the ritual for the Dark, information given to Basira by Elias. They meet Manuela Dominguez, who is guarding what is left of the Dark Sun. Jon looks at the Dark Sun despite Manuela's warnings, and he collapses after looking at it. The star is extinguished.
Martin gets a statement from a woman claiming to have been harassed by Jon. After finding out Jon forced the statement from her and subsequently appeared in her dreams, Martin delivers the tape to Daisy, Melanie, and Basira. The three hound Jon, and he admits to forcing and 'feeding' on the statement of five people total, including the aforementioned woman from MAG 142. Basira calls Jon a danger and a monster, and Jon admits he's not sure he can control it. He worries he might be being controlled by the web.
After going to the house on Hill Top Road and reading a statement from Annabelle Cane, Jon confessed he's not being controlled. Taking live statements feels good and even though he could stop, he doesn't want to. He feels guilty feeling that way. Under the watch of the girls, he stops taking live statements and records more 'stale' ones. It doesn't feed his hunger, but it stops him from starving. Similar to post-coffin Daisy, he goes through a withdrawal and is constantly weak and hungry.
Jon looks through a box of Gertrude's old tapes and tries to focus on the ones he isn't drawn to. One particular tape he has trouble forcing himself to press play. The tape is the statement of Eric Delano, and details his method to escape the hold the Eye has over him - to remove his eyes. Jon curses, but confronts Martin with the idea, asking him to gouge their eyes out and run away together. After being rejected, he presumably tells the girls the method, of who only Melanie ends up going through with it.
Finding a tape left on his desk, Jon discovers Martin has gone with Peter Lukas to the center of the tunnels under the Institute. He tries to get help from several different people, but ends up going alone after the Institute comes under siege by Julia Montauk, Trevor Herbert, and Not-Sasha. Jon is guided to the panopticon in the center of the tunnels by Elias, who tells him Peter has taken Martin into the Lonely. Jon goes in after them.
In the Lonely, he finds Peter Lucas, who tries to dissuade Jon from finding Martin and convince him that if he stayed in the Lonely, he wouldn't be able to hurt anyone else. Not fooled, Jon compels a statement out of him. Peter refuses to tell Jon what Elias' plans are though. Jon compels him so hard that the act of defying the Archivist kills Peter. Jon finds Martin and together they leave the Lonely.
MAG 160 sees Jon and Martin in one of Daisy's safe houses in Scotland. Jon reads one of the statements Basira brought him while Martin goes for a walk. The statement starts off with the usual - name of the statement giver and description of events - but it's revealed that Elias put that there as a front, and the real statement is Jonah's Magnus retelling of events. Jon is compelled to read the letter, and is physically harmed if he tries to stop. Jonah reveals that his ritual required the Archivist to have an encounter with every Fear entity, and lists the ones Jon has had, the Lonely being the last one. Jonah explains every other ritual has failed because they attempted to bring just one Fear into the world, when all the Fears are connected. Jon is forced to read an incantation, and every Entity is brought into the world at once.
- Persona - When recording a written statement, the Archivist takes on the voice and persona of the statement giver, reading the story with audibly different tones of voice and occasionally changing pitches to match the statement giver's. The Archivist is notably absorbed in the statements, becoming irritated if interrupted. Jon has shown worry over Martin reading multiple statements, possibly insinuating it's the statements themselves that effect the reader.
- Compulsion - The Archivist is able to compel others to answer a question or give a statement. It's implied that it can be taken a step further and compel someone to physically do something against their will. It's possible to resist compulsion, but almost everyone who has successfully resisted has been affiliated with an Entity, or is an Avatar themselves. In MAG 92, Elias describes the feeling of being compelled as 'quite nice' and 'tingly.'
- Knowing - The Archivist is able to Know certain things without having prior knowledge of them. This most often happens with relevant information to statements or the situation at hand. Jon has experienced pain while purposely trying to Know what an entity is planning.
- Understanding - Jon has been shown to understand written and spoken languages he's never learned. It's unclear but improbable if he can respond in those languages, as he's only even spoken English.
- Archivist's Presence - When the Archivist is present in the Archives, statement givers are able to elegantly and coherently tell their stories in a narratively interesting statement, regardless of their background. This is highlighted in MAG 100 when Jon is absent from the Archives and cut off from the Beholding. The statement givers tell short, curt statements, often getting off topic or needing encouragement to tell details.
- Inhuman Healing - The Archivist recovers from physical wounds remarkably fast. The more powerful the Archivist becomes, the quicker the wound heals. When Jon tries to cut his finger off, the cut heals as soon as he withdraws the knife.
- Feed Your Patron - When the Archivist reads a statement, wounds heal faster. Jon was able to recover enough from his coma to be able to leave the hospital after reading just one statement. It's a double-edged sword, however. After Jon stops forcing live statements from people, he gets weak and hungry, going through a sort of withdrawal. Jude Perry used the phrase "Feed [your god]... or it will feed on you." Similarly, when Jon is away from the Archives for weeks without reading a statement in MAG 107, he reports feeling sick, dizzy, and confused, and admits feeling better after reading it.
- Reliving Nightmares - After statement givers tell their story to the Archivist, they frequently relive their experience in a nightmare, sometimes taking on the roles of the creature they saw. The Archivist shares these dreams and is always present, observing the statement giver but never interfering. Elias reveals in MAG 120 that Jon has these dreams every night, cycling through those who have given their statements.
- Convenient Tape Recorders - A tape recorder seems to show up and start recording on its own whenever something relevant is happening, or a statement is being given. This most frequently happens around Jon, the current Archivist, but has happened to several other characters as well. Jon has said that he's stopped manually turning on recorders, assuming they'll record on their own if it's important. Unclear if this is a power of the Archivist or the Institute itself.
Marks from Entities
Jon has been marked in one way or another by every Entity. Almost every mark has been orchestrated by Elias Bouchard. Marks take the form of scars, injuries, or encounters. Elias has called Jon a "chronicle of fear" in reference to the gathering of these marks.
- Web - Jon's childhood encounter with Mr. Spider. He would've been eaten were it not for someone taking the Lietner away and getting enthralled in Jon's place.
- Corruption - Jane Prentiss' attack on the Archives, which left Jon with pock mark scars where the worms burrowed into his skin.
- Stranger - Not-Sasha's infiltration of the institute and Jon's close encounter with her, as well as the Unknowing.
- Spiral - Helen Richardson's statement drew the Distortion's attention to Jon. He has gone through the doors several times and been stabbed once by Michael. He's had multiple encounters with both version of the Distortion. Elias commented that Jon is deeply marked by the Spiral. 
- Hunt - Elias requested Daisy to investigate Gertrude's murder in the hope of an eventual confrontation with Jon.
- Desolation - Jude Perry, an avatar of the Desolation, gave Jon her statement and shook his hand, burning him.
- Vast - Mike Crew, an avatar of the Vast, gave Jon his statement and let him experience the sensation of the Vast firsthand.
- Slaughter - Melanie King, infected with a bullet that fueled her with rage, had stabbed Jon when he attempted surgery to remove it. Elias hired Melanie as a way of keeping her in the Archives until she could mark Jon.
- End - Jon's attempt to stop the unknowing left him in a coma where he was "all but brain dead." Elias was worried about Jon experiencing the End.
- Flesh - Jon had ribs two removed from Jared Hopworth, and avatar of the Flesh. 
- Buried - Jon's descent into the coffin to rescue Daisy. Elias purposely sent Basira away to give Jon a chance to go in.
- Dark - In Ny-Ålesund Jon looked upon the Dark Sun, a star left behind from the Dark's failed ritual. It was said that only powerful followers of the Dark could safely look at it.
- Lonely - Peter Lukas, an avatar of the Forsaken, had taken Martin into the Lonely, a pocket dimension of the Entity with the same name. Jon went in after them and killed Peter in the process.
As Jon is the main character of the show, he appears in almost every episode - thus it's easier to simply list the episodes he hasn't been in. Asterisks* mark episodes he still features prominently in as the subject; bold marks episodes where he isn't even mentioned.
- Jon is the only person to successfully complete a Ritual.
- As Jon develops more powers and becomes a stronger Archivist, he shows more empathy and genuine feelings - a parallel highlighting how the more monstrous he becomes, the more human he gets.
- Jon sings for just a few seconds in MAG 31 at the 13:25-14:15 mark (differs depending on where you listen to it). Jon's voice actor, the real Jonny Sims, is one of the lead singers in the Mechanisms.
- The Admiral is the only character Jon is ever recorded saying "I love you" to.
- Jon has been confirmed asexual, but Jonny Sims isn't sure what Jon would identify himself as, since he's not the kind of person to openly talk about feelings or sexuality.
- It's unclear which pronouns are correct for Jon, as all characters refer to Jon as 'him', but the description of MAG 132 has 'they.' This is the only time a description lists pronouns for Jon, and it's unclear whether this is simply referring to Jon's role of the Archivist or Jon himself.
- Before MAG 160 it was theorized that the Archivist must be marked be all the Entities for the Watcher's Crown, the ritual of the Beholding. This was backed up by Elias in MAG 92 saying it's the Archivist's job to experience things firsthand.
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- ↑ MAG 154: Bloody Mary
- ↑ MAG 106: A Matter Of Perspective
- ↑ 3.0 3.1 MAG 39: Infestation
- ↑ 4.0 4.1 MAG 22: Colony
- ↑ MAG 26: A Distortion
- ↑ 6.0 6.1 MAG 142: Scrutiny
- ↑ 7.0 7.1 7.2 MAG 81: A Guest For Mr. Spider
- ↑ MAG 3: Across the Street
- ↑ MAG 63: The End of the Tunnel
- ↑ MAG 1: Angler Fish
- ↑ MAG 107: Third Degree
- ↑ MAG 132: Entombed
- ↑ MAG 143: Heart of Darkness
- ↑ MAG 146: Threshold
- ↑ MAG 147: Weaver
- ↑ MAG 146: Threshold
- ↑ MAG 156: Reflection
- ↑ 18.0 18.1 18.2 MAG 157: Rotten Core
- ↑ MAG 102: Nesting Instinct
- ↑ 20.0 20.1 MAG 89: Twice as Bright
- ↑ MAG 92: Nothing Beside Remains
- ↑ MAG 158: Panopticon
- ↑ MAG 105: Total War
- ↑ MAG 131: Flesh
- ↑ MAG 122: Zombie
- ↑ MAG 142: Scrutiny
- ↑ 27.0 27.1 MAG 146: Threshold
- ↑ MAG 81: A Guest For Mr. Spider
- ↑ MAG 39: Infestation
- ↑ MAG 39: Infestation
- ↑ MAG 79: Hide and Seek
- ↑ MAG 160: The Eye Opens
- ↑ MAG 89: Twice as Bright
- ↑ MAG 91: The Coming Storm
- ↑ MAG 125: Civilian Casualties
- ↑ MAG 120: Eye Contact
- ↑ MAG 131: Flesh
- ↑ MAG 132: Entombed
- ↑ MAG 143: Heart of Darkness
- ↑ MAG 159: The Last
- ↑ MAG 160: The Eye Opens
- ↑ https://twitter.com/jonnywaistcoat/status/1009714615826157568?lang=en