In Normal, Illinois in 1958, Henry goes to his son's room at night and tucks him in. He notices that his father is wearing a pin with a symbol on it and asks what it is, and Henry says that someday he'll tell him about it. Henry says that he's going to work, winds up his son's music box, and lets it lull the boy to sleep.
Henry goes downstairs and enters a small building off the street. On the door is the same sign he has on his pin. A woman, Josie Sands grants him in a formal dress and they talk for a moment. A servant calls her into the next chamber and tells Henry that they'll be ready for him in a few minutes. As he waits, Henry hears screams and runs into the room. One man is clutching at his bleeding eyes, while another one tries to restrain Josie with an invocation. She ignores him and snaps his neck, while the blind man gives Henry a box with the symbol and tells him not to let Abaddon have it. Henry runs down the hallway to a workshop and mixes a potion using his own blood, and then paints a sigil on the door. The woman, Abaddon, tries to open it without success and the glyph glows with light, surrounding Henry...
... who finds himself in a motel room in 2013 with Sam and Dean Winchester.
Once Henry recovers from the shock, he asks the brothers which one of them is John Winchester. When they explain that they're not John, Henry wonders what he's done wrong. Dean demands answers and Henry says that violence isn't necessary. He apologizes for the misunderstanding and tries to leave, but Dean tries to handcuff him to the bed. When Sam goes to help, Henry manages to handcuff the two brothers together and runs outside. he's briefly overwhelmed by the sights of 2013, but notices the Impala and confirms that the date on the license plate is 2013. He prepares to steal the Impala but a maid frees the Winchesters and Dean orders Henry out of the car.
The brothers test Henry with holy water and confirm that he's not a demon. Henry says that they won't understand what's happening and Dean mentions that John is their father. Before Henry can respond, the hotel room vibrates and he tells them to get out. Abaddon steps out of the closet and tells Henry that she used the sigil and some of his blood to follow him through time. She telekinetically knocks Sam and Dean aside and advances on Henry, who tries to get through to the host. Abaddon laughs at him while Dean recovers and stabs her with the demon-killing knife. Much to his surprise the dagger temporarily injured Abaddon but doesn't kill her. Sam, Dean, and Henry run to the Impala and drive away. When the owner complains, Abaddon exudes a part of herself into him and reads his memories of Sam and Dean. Once she's done with him, Abaddon rips his throat open.
The brothers pull over outside of town and Henry vomits, unaccustomed to violence. He explains that he's from 1957 and that the woman is a demon. When he asks to talk to John, Dean tells him that their father is dead. When they wonder why he's interested, Henry tells them that John is his son.
The brothers go to a diner and confirm that Henry is who says he is. Dean reminds Sam that John thought that Henry abandoned him when he was a child and grew up hating him. Sam suggests that Henry may never return from 2013 but Dean isn't satisfied. They then talk to their grandfather and explain that they have the demon-killing knife. When they suggest sending Abaddon back to 1958, Henry explains that he had to use some energy from his soul to power the blood sigil. Sam is surprised that anyone other than an angel can do it, and Henry is puzzled that they John didn't raise them to be men of letters. The brothers explain that they're Hunters and Henry dismisses Hunters as crude amateurs.
Henry takes them to the house in normal but discovers that a comic book shop now occupies the place. The organization's symbol is still on the water and Henry figures that the Elders maintain the shop as a façade. As they go in, Henry continues talking dismissively of Hunters, explaining that they shoot first and ask questions later. The Elders had a select few Hunters that they gave their information to so they could destroy monsters. When Sam and Dean admits that they've never heard of the Elders, Henry figures that Abaddon killed them all in 1958.
As they go in, Henry explains that Abaddon wants the box, and shows it to the brothers. The Elders' phone number no longer exist so they borrow the punk clerk's laptop computer. As Henry takes in the computer in astonishment, Sam checks the names of the Elders that Henry has identified. He learned that four men all died in a fire at the "gentleman's club" in 1958. One man is named Albert Magnus, and Henry recognizes the name and says that they have to make a trip.
As night falls, the trio drives to the cemetery where the graves of the four dead men. Henry explains that Magnus refers to a famous alchemist and that someone put his name in the article so that any other elders would recognize it as an indicator to go to the graves. Three of the gravestones have the Elder's crest, the Aquarian Star, on them. The fourth one, belonging to Larry Ganem, has a Haitian symbol of the dead on it and Henry realizes that's the coffin they should open.
Abaddon goes to the comic book store and reads the punk clerk's memories. Once she has the cemetery's address that the clerk saw on the laptop, Abaddon release the girl, who begs for her life. The demon smiles and says that she likes her top.
Sam and Dean dig up and open Ganem's coffin and find a medal on it. It has a name, Tom Carey, that Henry doesn't recognize. He tells the brothers to put the coffin back as they found it and they return to the hotel. As Sam goes through John's journal, Henry whistles "As Time Goes By." When Dean remembers John whistling the same turn, Henry explains that he bought a music box with the tune to reassure John when he was frightened.
Sam finds an entry referring to Abaddon and Henry confirms that the demon is one of the Knights of Hell, hand-picked by Lucifer to serve him. Henry asks to see John's journal and explains that he was going to order one when he returned from his initiation. When he checks the journal, he discovers that his initials are inside it and realizes that he won't make it back to 1958. Sam tells his grandfather about how John thought his father abandoned him when he didn't return, and Dean angrily tells Henry that John grew up on his own without a father, and lost his wife and eventually his own life to demons. Despite that, Dean insists that John did more good than bad. Henry wishes that he had been there for his son but Dean tells him that he's too late for that. When Henry says that he was a legacy and he didn't have a choice, Dean tells him that his first responsibility was to his family.
As the brothers sleep, Henry goes through John's journal and looks at his grandsons. The next morning they wake up and discover that Henry is gone. He's left them a note saying that he's going to fix things but Dean worries that their grandfather will make them worse.
Henry goes to an apothecary and asks the clerk for the ingredients he needs for the blood sigil. When the clerk claims she doesn't know what he's talking about, Henry points out the Hunter signs painted on the window and admits that he knows she has no reason to trust her. She draws a shotgun and aims it at him but John uses a spell to render her unconscious.
Dean checks the Impala and confirms that Henry took one of the ingredients, an angel's feather, from the trunk. Sam checks the Internet and confirms that Abaddon killed the clerk at the store. Dean goes out to find Abaddon while Sam goes to Ganem's address, using the name on the medal. He talks to the old man and his housekeeper, and Larry explains that Abaddon killed the Elders on behalf of her master. Larry survived but was blinded by the demon, but he gave the box to Henry so that Abaddon wouldn't get it. When Sam wonders what the box signifies, Larry explains that it holds a key to the Elders' collection of scrolls and spells.
Dean finds the apothecary just as Henry did and finds his grandfather writing the blood sigil on the wall. Henry insists on going back to raise John and make sure he has the childhood he deserves. Dean admits that he was wrong about saying that Henry ignored his responsibilities and warns him that he can't change the past, but Henry insists on giving John the live he deserves.
When Sam asks Larry how they can stop Abaddon, Larry admits that it's impossible. However, he gives Sam the coordinates for a place where the key can be locked for good, since only it can be used to unlock the place. Sam is reluctant to steal away the knowledge for good, but Larry says that it's the other way. When Sam says that Dean has the key, the "housekeeper" knocks him out, transforms into Abaddon, and kills Larry with a knife. Abaddon then calls Dean on Sam's cell phone and offers to exchange Sam for the key and Henry. Dean has no choice but to agree and Abaddon tells him to meet her at a processing plant. Once he hangs up, Henry insists that he can travel back to 1958 and prevent it all from happening, but Dean refuses to take the chance with Sam's life. Henry ignores him and prepares to cast the spell, and Dean knocks him out.
That night, Dean drives to the processing plant with a handcuffed Henry. Dean tells him that he couldn't save John and he doesn't want to face Sam dying as well. He insists on doing anything it takes to save his brother. They go inside and Dean tells Abaddon to send Sam across while he sends Henry with the box. Henry refuses to go until Dean threatens to shoot him in the leg and make him crawl. Sam and Henry walk past each other and Henry ignores his grandson. However, Abaddon seals the doors and then rips out Henry's stomach. He reveals that he isn't really handcuffed, draws a gun, and shoots Abaddon in the head.
Unharmed, Abaddon laughs in triumph and searches Henry, only to discover that that he doesn't have the box. When she tries to exude a part of herself to read his memories, she discovers that she can't leave her body. The demon realizes that Henry and Dean inscribed a devil's trap on the bullet, trapping her in her body. Before she can attack, Dean decapitates her and tells the demon that since they can't destroy her, they'll cut her body up into pieces and bury them into concrete, with Abaddon trapped in the for eternity. Dean then goes to the dying Henry, who apologizes for judging them so harshly. He admits that he should have known better and says that he's proud of them... and of John for raising them the way they turned out.
Later, Sam and Dean bury Henry next to the other Elders. Sam says that he realizes now what Cupid said about how Heaven did everything it could to make sure Mary and John married. Dean shows his brother the photo that Henry carried of him and a young John, and wishes that John knew what really happened to his father. Sam wonders if it would have made any difference if Henry had been there for John, and Dean figures that John did the best that he could.