For over a thousand years, the Men of Letters gathered every object, scroll and spell they could find and hid it under one roof, a bunker in Lebanon, Kansas. The bunker was the safest place on Earth, warded against every kind of evil imaginable and was only accessible by a key which unlocked the front door.
After Father Max Thompson successfully came up with a way to cure demons, the Knight of Hell Abaddon was sent to kill him and stop his experiments. Abaddon tore Father Thompson apart, but not before he told her of the Men of Letters and their initiate Josie Sands who had filmed his first experiment in curing demons. Shortly after Father Thompson's death, Josie and Henry Winchester were sent to investigate apparent demonic possessions at a convent in Milton, Illinois where, unknown to them, Abaddon had created a "demon factory" where she'd steal people's souls to turn them into demons. Henry and Josie exorcised two of the demons, but Abaddon was immune and knocked Henry out. To spare Henry from possession after Abaddon learned that they were members of the Men of Letters, Josie volunteered to act as Abaddon's vessel instead and the amused Abaddon agreed. Abaddon possessed Josie, intending to use her to infiltrate, study and destroy the Men of Letters.
On the night of August 12, 1958, during Henry and Josie's initiation, Abaddon revealed herself and began massacring the Men of Letters. Witnessing the deaths of the Men of Letters elders after they failed to exorcise Abaddon, Henry is given a mysterious box by surviving elder Larry Ganem and told that Abaddon must not get it. Unable to escape Abaddon in 1958 and unaware of the extent of the devastation that will be wrought upon the Men of Letters that night, Henry uses a spell to travel forward in time in order to find his son John who he believes will be able to help him figure out the box and its purpose.
Henry arrives in the motel room of his grandsons Sam and Dean Winchester and demands to know where John Winchester is. Shocked, the Winchesters tell him neither of them are John and demand to know who Henry is. Confused by the fact that neither of them are John, Henry decides that the whole thing is a misunderstanding and decides to leave. The Winchesters refuses to let him and attempt to handcuff Henry to a chair, but Henry is able to handcuff them to the chair instead and escapes outside where he tries to steal the Impala. However, the Winchesters get themselves free and quickly recapture Henry. The Winchesters then test Henry with silver and holy water to test that he's not a monster or a demon and he comes back clean. Henry refuses to tell them anything, saying that what's going on is likely beyond their level of understanding. Dean demands to know why he shouldn't get violent when Henry came out of his closet, asked about his father and smashed the window of the Impala. Henry is stunned to hear that he's with his grandsons, but before they can discuss things further, Abaddon arrives through Henry's portal, taunting him over his shoddy spellwork. Abaddon demands the box, promising to kill Henry, Sam and Dean quickly if he turns it over, but Henry refuses. When Sam and Dean try to intervene, Abaddon flings them into the walls and stops Henry from moving. Henry tries to reach out to Josie to fight Abaddon's control of her body, but Abaddon just tells him that Josie is indisposed and its just them. At that moment, Dean stabs Abaddon in the back with the demon-killing knife, trying to kill her with it. However, while it causes her pain, the knife is not enough to kill her so the Winchesters take the opportunity to flee while Abaddon is recovering. They make a quick escape in the Impala, but their flight is witnessed by the motel clerk and Abaddon uses her powers to search his memories from which she gets a look at the Impala's license plate. Thanking the clerk, Abaddon slits his throat with her fingernails, killing him.
Getting a good distance away, Dean pulls the Impala over so that Henry can throw up and he and Sam demand answers from him. Henry informs them that the demon was Abaddon who is from Hell while he is from Normal, Illinois, 1958. Henry asks them once again to take him to John who he believes can clear the whole thing up, but Dean informs him that John is dead. When asked what's it to him, the grief-stricken Henry reveals that he's John's father. Reconvening in a diner, Sam and Dean are able to confirm Henry's identity with his driver's license and the facts that he knows about John. Dean isn't pleased to see him though as all they know about Henry is he ran out on John one night and never came back. Sam suggests that Henry didn't run out but rather got trapped in the future instead. Dean is still angry as John hated Henry for leaving him, but Sam points out that John wasn't a great father himself. Bringing food to Henry, they start asking him questions with Dean wondering why Abaddon didn't die when he stabbed her with the demon-killing knife. Henry tells him its because the only type of knife that can kill a demon is an ancient demon-killing knife of the Kurds and Dean tells him that's what their knife is and he got it from a demon. As they don't have a way to kill Abaddon, Sam suggests sending her back to 1958 and Henry tells them the ingredients he'd need for the spell as well as the fact that his soul would need a week to recharge, surprising them as they only thought angels used souls for power. Henry is surprised they don't know about that ability and asks them what level of knowledge they are in the Men of Letters. Sam and Dean inform him that John trained them to be hunters not Men of Letters which disgusts Henry as he sees hunters as apes.
At Henry's request, the Winchesters bring him to the club in Normal, Illinois where the Men of Letters headquarters was located, but it is now a comic book store called Astro Comics. Henry is shocked to see the club is now a comic book store and Dean demands answers on what the Men of Letters are. Henry refuses to tell them as he sees hunters as beneath him, but finally relents when Sam reminds him that they are also John's children. Henry explains the purpose of the Men of Letters and realizes that Abaddon must've done something as no one has ever heard of them. Entering the store, Henry explains that Abaddon was after the box Larry gave him, but he doesn't know what it is as Abaddon attacked before he could be initiated fully into the Men of Letters and be told all of their secrets. Dean points out that Henry came through time to protect a box that he knows nothing about from a demon he also knows nothing of, but Henry ignores him. Reaching the inside of the shop, Henry tries to use Sam's phone to call the Men of Letters emergency number, but Dean informs him that it doesn't work like that anymore. Henry insists that there must still be a surviving elder out there who can help them figure out what to do with the box and how to stop Abaddon so Dean borrows the store clerk's computer to look up the night of the massacre. Entering the names of the elders Henry gives him into a search engine, Sam finds a newspaper article which states that there was a fire the night of the massacre and four men perished in it. Henry knows it wasn't a fire but Abaddon and reacts when he hears that Albert Magnus was one of the men that perished that night. After looking up the graves of the murdered elders, the Winchesters leave the comic book store to find the graves. Awhile later, Abaddon arrives at the comic book store, hoping to find the Winchesters there since it used to be the Men of Letters headquarters. Abaddon reads the memories of the clerk and learns of their search for the Men of Letters graves and where they are. Liking the clerk's clothes, Abaddon kills her and takes the clothes for herself to replace her bloodstained dress.
Reaching Albert Magnus' grave, Henry explains that the name is actually Albertus Magnus, the greatest alchemist of the Middle Ages. The Men of Letters used his name while going incognito so Henry believes that someone planted the name in the article so that if a Man of Letters saw the article, they'd know something was amiss and come looking. Dean notices the Aquarian Star on Magnus' grave and Henry explains how its the Men of Letters crest. Checking out the other graves, Sam notices that Larry Ganem's grave doesn't have the symbol upon it. Instead, Henry spots the Haitian symbol for speaking to the dead and realizes that its the message they are looking for. He has Sam and Dean exhume the grave so that they can examine Larry's body. Inside the coffin, they find the body of a World War I officer, Captain Thomas J. Carey III which means nothing to Henry. Sam and Dean suggest that Larry may have survived Abaddon's attack and took on the officer's identity to hide out. Satisfied with their findings, Henry has them rebury the body.
Heading to a nearby motel, Dean searches county records and discovers that Tom Carey is still alive at 127 years old and is living in Lebanon, Kansas. Dean suggests they get some sleep before going to meet him, but Sam finds something important in John's Journal: John once tortured a demon that worked for Abaddon and the demon told him that Abaddon is a Knight of Hell. Henry informs them that the Knights of Hell are an elite order handpicked by Lucifer himself from amongst the very first demons which, as Sam points out, means they are pure evil and very strong. Henry explains that according to legend, the archangels killed all of the Knights, but Abaddon's survival shows that not to be true. Dean suggests instead that Abaddon is the last of her kind. Taking a look at John's journal, Henry sees that it was the one he ordered for himself before his final initiation and realizes that he doesn't make it back to his own time. Sam and Dean tell him they don't know for sure, they only know that John never saw him again and that John thought that Henry had run out on him. Henry is upset as he should've been there to teach John the ways of the Men of Letters, but Dean angrily informs him that John learned things the hard way from his lonely childhood, fighting in the Vietnam War, losing his wife to a demon and then losing his own life to a demon as well. Dean tells Henry that John had a bad time of it, but he kept going and in the end he did more good than he did bad in the world. Dean is furious as Henry, while upset with abandoning John to that, tells him that it was the price he had to pay for upholding great responsibility. Dean tells Henry that his responsibility was to his family, not a glorified book club. When Henry tells him that he was a legacy and had no choice, Dean storms out. Wanting to learn more about his son, Henry reads the journal as the Winchesters sleep and becomes determined to fix the past to be there for John.
The next morning, Henry leaves Sam and Dean a note stating that he will fix everything and breaks into the Impala's trunk, steals an angel feather and leaves. Henry travels to a nearby hoodoo shop to get the remaining ingredients that he needs to return to the past. When the shopkeeper won't sell to him, Henry uses a spell to put her to sleep. Henry collects the necessary ingredients and starts casting the spell, but is interrupted by Dean. Henry insists that he needs to go back to his own time even if he doesn't survive it as he needs to save John. Seeing what John's life was like from his journal caused Henry great pain and he feels that he abandoned John like Dean had said. He intends to go back and give John the life he deserved, not the one that he was forced to live. Dean insists that it might not be meant to be, but Henry believes its the right thing to do and that by going back to an hour before the attack and preparing, he can stop Abaddon and save John. Even though saving John like that might erase Sam and Dean from existence, Henry still believes its the right thing to do, telling Dean there might not be an Apocalypse for them to stop if he does this. As Dean argues with Henry, Abaddon calls him to inform him that she has Sam hostage. Abaddon demands that he trade Henry and the key for Sam or she'll kill Sam and Dean reluctantly agrees. Henry insists on trying to go back in time and stopping all of this from happening, but Dean isn't willing to take the chance that he will fail with Sam's life on the line and knocks him out.
After waking up and finding Henry gone, Dean calls Garth to find out about any local shops that sell real hoodoo while Sam finds out about the comic book store clerk's murder which they realize must be Abaddon's doing and that it means that she must be close. Dean goes after Henry using a location Garth gave him while Sam goes to Larry's house to find out what's in the box and how to stop Abaddon. Sam tells Larry that Henry is dead, but he'd found Henry's journal and was hoping Larry could explain what happened the night Abaddon attacked the Men of Letters. Larry tells him it doesn't matter as Abaddon slaughtered the entire Men of Letters order that night and was a "hired gun." Larry alone survived, but was left blind by Abaddon's attack. Sam tells Larry that Abaddon is back and is after the box and asks what's inside it. Larry explains that its "the key to every object, scroll, spell ever collected for thousands of years under one roof. It is the supernatural mother lode." Sam realizes that Abaddon wants the key in order to get her hands on that "motherload" and Larry tells him that Abaddon can do untold harm with it. However, when Sam asks how they stop Abaddon, Larry tells him that he doesn't and writes down a set of coordinates. Larry tells Sam to take the key there, throw it inside and lock the door forever behind it. Larry explains that due to the place's defenses, with the key locked inside, no one would ever be able to gain entry again and it could never be used for evil. While Sam is shocked at this idea, Larry tells him that's the price they have to pay to keep it from Abaddon. Sam informs Larry that while he doesn't have the key, his brother does and Larry's wife reveals herself to be possessed by Abaddon. Abaddon knocks Sam out and then kills Larry and his wife before returning to Josie's body.
Henry wakes up on the way to the rendezvous with Abaddon and Dean convinces him to help save Sam. Henry carves a devil's trap into a bullet and loads a gun with it. Dean warns him that to do what they plan, Henry will have to get close to the demon and it could get ugly, but Henry is willing to take the risk to protect his family. Arriving at the processing plant where the meeting is to take place, Dean makes it seem like Henry is handcuffed so that Abaddon won't get suspicious.
Acting, the two enter the plant with Henry pretending to be angry that Dean would do such a trade, telling him that hunters are short-sighted. Dean rebukes him by reminding Henry that they aren't extinct unlike the Men of Letters. Dean puts the box into Henry's pocket and tells Abaddon he'll send Henry at the same time as she sends Sam. Abaddon agrees and promises that there will be no tricks and she will let them go afterwards. Dean threatens Henry to get him moving and he refuses to hear Sam's apologies. Sam tries to convince Dean that the whole thing is a bad idea, but Dean insists on leaving. As they try, Abaddon goes back on her word and locks them in, telling them that she lied. Abaddon then plunges her hand into Henry's abdomen, but he takes the chance to shoot the devil's trap bullet into her head. Abaddon doesn't realize what Henry's done and pulls out what she believes to be the box, but instead finds it to be a pack of playing cards. Abaddon tries to read Henry's memories, but finds she can't and that she's stuck as Sam rushes to support Henry. Abaddon realizes what happened and gloats that they still haven't killed her, but Dean tells her that she'll wish they did. Dean decapitates Abaddon with a machete and informs her that the devil's trap bullet will keep her trapped in Josie's body, allowing them to cut her into pieces and bury her in cement, thus forever entombing her. Dean tells Abaddon she may not be dead, but she'll wish she was.
Dying, Henry makes amends with his grandsons, telling them that they may be hunters, but they are also Winchesters and as long as the Winchesters are alive, there's always hope. Henry tells them that just by meeting them, he knows he'd be proud of John as a man. After handing Sam the box, Henry dies of his wound.
Following Henry's death, Sam and Dean bury him with the other Men of Letters who died at Abaddon's hands. Sam finally understand what Cupid said about Heaven working so hard to get their parents together: they were trying to bring together the Winchesters and the Campbells, the brains and brawn of the hunting world. Dean is saddened by the fact that John will never know the truth that his father didn't run out on him but instead got sent to the future where he saved his grandsons' lives. The two wonder about what would've happened if John had Henry growing up and decide to look for the place the key they fought so hard to protect goes to as they are Men of Letters Legacies. Shortly afterwards, the Winchesters use Larry's coordinates to find the Men of Letters bunker, the place the key went to. They then moved into the Bunker and made it their new base, taking on the role of Men of Letters themselves.
Following her defeat at the hands of the Winchesters, Abaddon is cut into pieces and buried in cement as Dean promised. However, while doing the Third Trial, Sam and Dean discover that they need to cure a demon. Needing a demon to try it out on, they put Abaddon back together, but while they are distracted by a phone call from Crowley, she is able to remove Henry's devil's trap bullet and escape. Free once more, Abaddon began a crusade to take over Hell for herself that is only stopped when Dean finally kills her with the First Blade.
- This features the first time a devil's trap bullet is used on the show. Dean and Tracy Bell later attempt to use them against Abaddon again, but she blocks the bullets with a bulletproof vest. Abaddon uses such a bullet on Crowley to keep him out of her final fight with Dean, and Sam uses one on Crowley when he tries to kill Crowley as part of his deal with Rowena.
- When Abaddon uses a devil's trap bullet to incapacitate Crowley during her final battle with Dean, she tells him about how she got the idea from when Henry used it to defeat her.
- Following this battle, Abaddon focuses on taking over Hell and ignores her former quest for the key.