After being killed by Dick Roman, hunter Bobby Singer became a ghost to look after Sam and Dean Winchester who had been like family to him. Bobby remained a ghost for months, aiding in the fight with the Leviathans where he could, but eventually started turning into a vengeful spirit. As a result, he had the Winchesters burn his flask and put him to rest. While the Winchesters and Bobby believed that would be the end of it, the King of Hell Crowley paid rogue Reaper Ajay to take Bobby's soul to Hell instead of Heaven where it belonged even though his deal had been broken, citing all the damage Bobby had done to his kind over the years. In Hell, Bobby was locked in a cell in a dungeon-like area of Hell where he was tormented by demons visiting him all day in Sam and Dean's forms.
Following the discovery of the Demon Tablet and what it contained, the Winchesters set to work on closing the Gates of Hell forever. To this end, Sam undertook the Trials of God, the first of which had him kill a hellhound and bathe in its blood.
Under intense stress, Kevin began hallucinating Crowley talking to him in his sleep and called Sam and Dean in a panic about it. After they show up, they get him to calm down and reveal the second trial that he has translated to them: rescue an innocent soul from Hell and deliver it unto Heaven.
To figure out how to get into Hell, Sam and Dean decide to summon a Crossroad Demon for information. They place a devil's trap around the crossroads they summon the demon at so that when he appears, displeased to see them, the demon is trapped and can't leave. The Winchesters take the Crossroad Demon to an abandoned building where they use holy water to torture a way into Hell out of the demon. The demon refuses to tell them, saying that its a secret and he'll be killed for telling them. After they continue to torture him, the Crossroad Demon breaks and finally tells them that for a price, rogue Reapers can smuggle them across Hell's border as they've got secret ways into and out of the Veil, Heaven and Hell and can smuggle both souls and people. The Crossroad Demon then begs them to kill him as he feels its better for him to be dead than have to face Crowley. Dean agrees, but has the demon tell them everything about the rouge Reapers and where to find one before he kills him.
Going to the location given to them by the Crossroad Demon, Sam and Dean find the rogue Reaper Ajay and approach him for help. Ajay is surprised they want to do business as they are mortal, but hears them out. The Winchesters ask Ajay to help them get into Hell on a "visitor's pass" which surprises Ajay as no one wants to get into Hell. When pressed however, he admits that he could do it and wants the Winchesters to owe him a favor one day in return as they are resourceful. When Sam points out that he acts like he knows them, Ajay tells them that he knows that they are the Winchesters. When Dean asks if they've met, Ajay reveals that he is the Reaper who took Bobby Singer to Hell which surprises them as Bobby should've ended up in Heaven. Ajay explains that Crowley paid him to take Bobby's soul to Hell instead of Heaven when he was put to rest. Determined to rescue Bobby, Dean asks how much they have to pay for two tickets down and three back, but Sam convinces him that he has to rescue Bobby and do the Trial solo. Once informed that only Sam is going, Ajay has Sam follow him and informs Dean that Sam will be back in precisely twenty-four hours time. Ajay leads Sam into a nearby alleyway and teleports them away. Unknown to them all, the whole exchange was watched by a homeless man who is in actuality a demon spy for Crowley.
To Sam's surprise, instead of bringing him directly to Hell as he expected, Ajay brings him to Purgatory instead. Ajay tells Sam that Purgatory is Hell-adjacent and gives him directions to a portal into Hell, unwilling to enter Hell himself with a Winchester due to the risks. Ajay orders Sam to be back in precisely twenty-four hours and returns to Earth leaving Sam alone to find his way to the portal to Hell.
On Earth, Ajay returns to his cab a few hours later with food to find Crowley waiting for him. Crowley questions Ajay about his deal with the Winchesters, having heard about it from his spy. Ajay fearfully admits that he made a deal with Sam as he occasionally moonlights as a freelancer. Crowley is furious at the idea that Ajay would freelance for the Winchesters. When questioned, Ajay tells him that Sam wanted to get into Hell but he doesn't know why as Ajay doesn't ask questions. After Ajay tells him that he's supposed to pick up Sam in seventeen hours, Crowley kills him with an angel blade in hopes of stranding Sam.
In Purgatory, Sam gets attacked by a vampire but is able to kill it with its own Purgatory Blade. Armed with both the Purgatory Blade and the demon-killing knife, Sam locates the portal soon afterwards and enters Hell.
In Hell, Sam makes his way through a dungeon-like area filled with souls pleading for help. Sam eventually finds Bobby who punches him in the face upon arrival, believing him to be one of the demons that are sent in Sam and Dean's form to torment him. Sam is eventually able to convince Bobby that its really him by telling him something only he and Dean would know: Bobby's love of Tori Spelling and his pedicure at the Mall of America that changed his life. Relieved, Bobby embraces Sam, telling him he's the 200th Sam he'd seen that day alone. Bobby worries for a moment that Sam has died and came to Hell himself, but Sam reassures him that its a rescue mission instead and arms him with the demon-killing knife. The two begin to make their way out of Hell, but come under attack by two demons. Bobby kills the one that Sam is fighting and then kills the other one. However, a third demon takes on the form of Sam to confuse Bobby, leaving him to choose which one to kill. Finally, Bobby kills the one to his left which proves to be the demon Sam. When asked by Sam, Bobby admits he didn't know it was actually the demon Sam, he just took the chance it was since it was a 50/50 chance. The two continue their run down the corridor and find the portal and make their way out of Hell and into Purgatory.
At the same time, Crowley realizes that everything that is happening means the Winchesters are up to something and orders his demons to find Kevin. While Crowley is doing this, the pressure starts to get too much for Kevin and he hides his half of the demon tablet to take some of the pressure off of him. Kevin defiantly refuses to tell Dean where to find the tablet and while he's dealing with that, the angel Naomi appears. However, Dean is not receptive to her as he knows that she mind controlled Castiel into spying on them and trying to kill him. Naomi claims that she was simply trying to reach out to Castiel and in a mentally unstable condition, he misinterpreted her actions as having him spy on the Winchesters and try to kill Dean when ordered to protect the angel tablet at all costs. Naomi claims that she's a warrior and protecting Heaven is her job and as such she's scared for all of them with Castiel on the loose with the angel tablet. However, Dean doesn't believe her lies, telling her that he doesn't trust angels and as such, he doesn't trust her. Naomi points out that despite that, Dean hasn't warded Garth's houseboat against angels, hoping that Castiel will return to him. Naomi insists that they are on the same side: closing the Gates of Hell and getting Castiel back. Insisting that they can be of help to each other, Naomi tells Dean that Ajay's way into Hell is through Purgatory, something she knew he'd like to know. She then leaves.
Following Naomi's revelation, Dean checks on Ajay only to find him dead. Knowing that there's only one way to get Sam out of Purgatory, Dean contacts Benny Lafitte for help. Meeting in the alley where Sam and Ajay entered Purgatory, Dean asks Benny to allow Dean to kill him so that Benny can return to Purgatory and show Sam the way out like he did Dean. Dean knows he's asking a lot, especially since he hasn't been there for Benny lately, but Benny agrees to help to Dean's surprise. Benny tells Dean that Sam's his brother and that Benny could use a break from the world. Benny explains that its been tough on him as he doesn't fit in with the humans or vampires and not belonging anywhere is wearing on him. Dean promises that when Benny gets back he'll change all that and tells Benny to ride out with Sam like he did with Dean so Dean can resurrect him again. Benny agrees and after a tearful goodbye, Dean decapitates Benny with a machete, killing him and sending his soul back to Purgatory. Unknown to Dean, Crowley's demon spy hears the whole thing and reports it all to Crowley.
Reaching Purgatory, Bobby is not happy to learn where they ended up. The two travel to the spot where Ajay is supposed to pick them up and Sam explains the Trials to Bobby and how they only have one left after this one but Kevin has yet to translate it. Bobby suggests bringing him back to continue helping them, but Sam tells Bobby that as much as he'd like that, for the Trial to work, Bobby's soul has to enter Heaven and even if it didn't, they have no way to tie him to the Earth. Bobby is disappointed as he thought oblivion awaited him once he got his Hunter's Funeral and is distrusting of Heaven, but agrees to do his part to help, asking Sam to bring him back if they do find a way. Sam gets worried when he realizes that they've reached the spot where Ajay is supposed to meet them at the exact time and he isn't there. While Bobby thinks Ajay might just be a little late, Sam points out that he was specific to the minute and that for him not to be there, something must be wrong and they have no way out without him.
Sam and Bobby wander Purgatory looking for a way out and Bobby comments on how hard it must've been on Sam for him to not be able to get Dean out for a whole year. When Bobby learns that Sam didn't even try, he is upset, but they are interrupted when three vampires attack them. Sam kills two before Benny shows up and rips the throat out of the last one. Sam stops Bobby from attacking Benny who explains that Dean sent him to get them out. Bobby is disgruntled at the idea of working with a vampire and that Dean actually befriended one, but reluctantly agrees to follow Benny. Benny leads Sam and Bobby to the same portal he and Dean used to get out which opens once again when it senses Sam's presence. Sam tells Bobby to go straight to Heaven when he reaches Earth and not to stop to say goodbye which agrees to, saying there's no reason to believe they won't see each other again someday. Sam casts a spell that sucks Bobby's soul into his arm, but when he turns to Benny to do the same, Benny hesitates. At that point, three more vampires arrive and Benny leaves to hold them off, telling Sam he was never any good on Earth anyway and to tell Dean he said goodbye. Respecting Benny's wishes, Sam tosses him the Purgatory Blade he took off the vampire earlier and Benny kills one vampire and faces off with the other two. Sam enters the portal and watches as Benny continues to battle the vampires as the portal closes and sucks him back to Earth.
In the 100-Mile Wilderness in Maine, the portal from Purgatory drops Sam back on Earth where Dean is waiting for him. Sam tells Dean he got Bobby out, but not Benny and explains how Benny stayed behind to hold the vampires off, though Sam thinks he would've stayed anyway even if they hadn't shown up. Although saddened, Dean tells Sam its time to put Bobby back where he belongs and Sam casts a spell to send Bobby's soul to Heaven. However, Crowley appears and captures Bobby's soul, trapping it in a red and black cloud not far off the ground. Sam and Dean are pissed to see Crowley, telling him that Bobby doesn't belong in Hell. Crowley tells them that Bobby does if he says he does, claiming that with the untold damage Bobby inflicted on demons, Hell is too good for him. When the Winchesters rush him, Crowley simply pins them to two trees and starts to pull Bobby's soul back to Hell. However, Naomi intervenes and stops the descent of Bobby's soul, telling Crowley that his stopping the Winchesters from rescuing an innocent soul from Hell is not right. Crowley tries to convince Naomi to stop helping them, telling her that before the Winchesters are done, they'll both be locked away. Naomi informs Crowley that she only cares that he's locked away and she'll figure out the rest. Crowley calls Naomi a bureaucrat and tells her that she's fighting outside of her weight class. Enraged, Naomi starts to use her holy Photokinesis on Crowley, but he quickly flees, freeing Sam and Dean. Naomi then cancels Crowley's spell and Bobby's soul rises to its rightful place in Heaven. Naomi reminds Dean she told him he could trust her and then leaves herself. With Bobby's soul in Heaven, Sam casts the spell to officially end the Second Trial.
The effects of the Second Trial take a worse toll on Sam, causing him to be weak at times to the point of being unable to shoot straight and then causing him to collapse with a high fever when near Metatron.
Shortly after Bobby is rescued, Crowley finally locates Kevin on Garth's houseboat, telling him that he found his mother and she gave Kevin up under torture. When Kevin insists she wouldn't do that, Crowley admits that's true and that instead they killed Linda and got Kevin's address off her smartphone. Crowley then kidnaps Kevin once again for his own purposes, but its later revealed that he lied about having killed Linda and is actually holding her captive.
After sending Bobby to Heaven, Dean informs Sam that he buried Benny's body instead of burning it after he killed him as it didn't feel right after he sacrificed himself to get Sam out of Purgatory. To Dean's surprise, Sam agrees with this move, his view of Benny having been changed by his sacrifice and tells Dean to leave the door open to bring Benny back if he wants to. Shortly afterwards, they find Kevin and everything of his gone, taken by Crowley when he kidnapped Kevin, though Crowley left no sign that he was ever there, leaving them without the tablet or a way to figure out the Third Trial.
After being rescued, Bobby made it into Heaven and got his own private Heaven made up of his house where he is happy, although bored as he has nothing to do before Sam and Castiel contact him for help with breaking into Heaven to break Metatron out.
Years later, after returning to Purgatory in search of the Leviathan Blossom, Dean asks a Leviathan about Benny. The Leviathan reveals that Benny is dead, ripped apart by the vampires for his actions. Dean is devastated to learn about this after all that Benny did for him and how Benny had sacrificed himself to get Sam out of Purgatory.