After learning that the Gates of Hell can be closed from the Prophet Kevin Tran, Sam begins the Trials of God to close the Gates forever using information from the demon tablet. After the angel and Scribe of God Metatron rescues Kevin from Crowley, the Winchesters learn that the Third Trial is to cure a demon.
With the information on the last Trial, Sam and Dean set out to find out how to cure a demon with help from their angel friend Castiel, eventually learning of a ritual devised by Father Max Thompson. Needing a demon to do it on, the Winchesters put back together the Knight of Hell Abaddon they had trapped in the body of Josie Sands and then cut to pieces to imprison due to their inability to kill her. After they have learned that Abaddon had been the one to kill Father Thompson, Crowley calls the Winchesters, leading to Abaddon discovering that a "salesman" now rules Hell, enraging her. While the Winchesters are distracted with their phone call, Abaddon is able to pull the devil's trap bullet binding her from her mouth and escape. At the same time, the Winchesters learn of Crowley's attack on people they've saved. As he kills Sarah Blake, Crowley demands that they give up the Trials in exchange for his stopping his attacks. Though Sam considers surrendering, Dean convinces him to keep going.
Continuing his attack on the people they've saved, Crowley goes on a blind date with Sheriff Jody Mills and after emotionally manipulating her, uses a hex bag and spell to place a hex on Jody so she will cough up blood until she dies. Dean calls Crowley who informs him that he has one minute until Jody is dead and Dean agrees to stop the Trials if Crowley spares Jody. Crowley demands the whole demon tablet as well which Dean agrees to with the stipulation that Crowley exchange it for the angel tablet as Crowley shouldn't be allowed to have that much power. Crowley agrees if they say "I surrender" and once Dean does, Crowley calls off his attempt on Jody's life. As a result, Jody survives.
Needing the full demon tablet, Sam and Dean contact Kevin Tran who meets them where he hid his half of the demon tablet during the Second Trial. Kevin digs up the first half of the demon tablet and then puts it back together with the second half of the demon tablet, repairing it. Kevin gives the demon tablet to the Winchesters who give him the key to the Bunker where he can stay in safety until everything is over. As they leave, Kevin reassures them that they're doing the right thing.
Following Crowley's instructions, the Winchesters travel to Singer Salvage Yard in Sioux Falls, South Dakota, a place owned by their deceased friend Bobby Singer. There, Crowley greets them and the Winchesters show him that they have the demon tablet while Crowley shows them that he did bring the angel tablet as promised. Crowley pulls out a massive contract that Dean is suspisous of, but Crowley tells him that the highlights are that they swap tablets, the Winchesters stop the Trials forever and he stops killing everyone they've ever saved. Dean goes to sign the contract, but Crowley demands that Sam do it as Sam is doing the Trials. Dean only agrees to do it if he can check over the contract for fine print which Sam reluctantly agrees to. Dean reads the contract, moving ever closer to Crowley under the pretext of reading higher up the contract. Crowley taunts Dean the entire time about how their humanity is the reason he keeps defeating the Winchesters and tells Dean to let Sam sign the contract after Dean has finished reading it. At a nod from Sam, Dean slaps a pair of handcuffs on Crowley, connecting him to Dean. Crowley is amused at first, but suddenly discovers that his powers no longer work. Dean shows him that the handcuffs are engraved with binding sigils and a devil's trap. Dean tells Crowley that the handcuffs will keep him from using any of his powers or smoking out. Crowley punches Dean to little effect and Dean punches him back and takes the angel tablet from him. Dean tells Crowley that he can keep it up as Crowley is now "our bitch" and that that means that "your demon ass is going to be a mortal ass." When Crowley asks Sam what Dean means, Sam tells Crowley that he's the Third Trial.
Having captured Crowley, the Winchesters take him to an abandoned church where Sam prepares weapons in case any demons come looking for Crowley while Dean chains Crowley to a chair in the church, leaving the handcuffs on and paints a devil's trap around him to further hold him. Sam then enters the church to make his confession as part of the ritual while Castiel arrives looking for Dean's help. Castiel reveals that he is working with Metatron on the Trials to seal Heaven and that Metatron has been captured by Naomi. As a result, Castiel asks for Dean's help in finishing the Angel Trials. At the insistence of Sam, Dean reluctantly agrees to go with Castiel while telling Sam to start without him and if he's not back in eight hours, finish the job.
After Dean and Castiel leave, Sam injects Crowley with the first dose of purified blood despite Crowley's taunts that it won't work. Moments later, Sam's arms start glowing from the power of the Trials as he comes closer to completing them. The next hour, Sam injects Crowley with more blood, but Crowley takes the opportunity to bite Sam's arm, apparently to get back at him. After punching Crowley, Sam heads out to the Impala to get a bandage. While he's gone, Crowley spits Sam's blood from his wound into his hand and uses it to call Hell to ask them to send someone to rescue him.
Hours later, as Sam prepares another injection, the church suddenly starts to shake and the floorboards crack through the devil's trap, breaking it, through Crowley remains restrained by the handcuffs and other restraints placed on him. Believing this to be his rescue, Crowley taunts Sam, telling him he can't kidnap the King of Hell and not expect anyone to notice. The doors burst open and the Knight of Hell Abaddon arrives to Crowley's surprise as he'd believed her to be dead. Abaddon tells Crowley she is the only one that's come and flings Sam into the church wall with telekinesis when he tries to shoot her. Crowley is pleased, commenting that sending in a Knight of Hell is better than sending in a few "grunts". Abaddon flings Sam through the church window, but refuses Crowley's order to untie him so he can kill Sam himself. When Crowley tells her that he's her King, she punches him and tells Crowley that she was shocked to arrive in 2013 and find that Crowley was in charge of Hell, beating on him all the while. Crowley tries to reach for Sam's gun after he is knocked to the ground, unable to defend himself otherwise due to being restrained, but Abaddon sends the gun out of his reach. Despite Crowley trying to warn her about Sam's efforts to shut the Gates of Hell, Abaddon is more concerned with discussing a "regime change" with Crowley, kicking him in the face hard enough to knock him out after he calls her a whore. As Abaddon turns around, a recovered Sam, unable to kill her, douses Abaddon in holy oil. Before the stunned Abaddon can react, Sam sets her alight in holy fire. While the holy fire can't kill Abaddon, it causes her such extreme pain that Abaddon abandons her vessel Josie Sands and flees the church in her smoke form.
With Abaddon gone, Sam rights Crowley and repairs the devil's trap as Crowley compliments him, showing signs of humanity. Despite Crowley's objections due to them fighting Abaddon "together", Sam gives him his next dose of purified blood and Crowley yells about wanting to be loved, showing further signs of humanity. The next hour, as Sam prepares the next injection, Crowley begins wondering how, given his evil history, he can even begin to look for forgiveness for his actions. Sam suggests that Crowley start with cooperating with the demon cure and Crowley willingly allows Sam to administer his next injection.
After getting the Cupid's Bow that they need, Dean and Castiel are approached by Naomi who tells them she is not there to fight but to talk. She warns them that she learned from Metatron's mind that he intends to expel the angels from Heaven onto the Earth as God kicked Lucifer out of Heaven. Naomi insists that she's telling the truth and though Castiel refuses to believe her, Dean chooses to. Naomi warns Dean that if Sam completes the Trials, he will die as God intended for the one doing the Trials- the ultimate sacrifice. After begging Castiel not to continue down his path and promising to listen if he truly wants back into Heaven, Naomi departs. After Naomi is gone, Dean asks Kevin, who was listening to the whole conversation through the phone, to check the angel tablet to see if Naomi is telling the truth. When Kevin can't find anything, Dean has Castiel bring him back to the abandoned church where Sam and Crowley are. Still believing himself to be on the right path, Castiel departs to continue his work.
Sam completes the injections and recites the modified exorcism needed to complete the curing ritual. His arms glowing more than ever, Sam goes to finish the job when Dean bursts in and stops him. Dean tells Sam that Metatron lied and Sam will die if he completes the Trials, but Sam doesn't care, telling Dean that they are so close to ending the threat from demons forever and he needs to finish it or more people will die. Dean reminds Sam of what they've learned since starting the Trials: how to kill a hellhound, how to rescue souls from Hell and now how to cure demons. Dean believes that with that knowledge, they can turn the tide but he can't do it without Sam. Sam, however, feels that he just keeps letting Dean down and he can't keep doing that and believes that by finishing the Trials he can keep that from happening again. Dean tells Sam that there is nothing past or present that he will put in front of Sam and reminds him of the things he's been willing to do to keep Sam by his side. Sam finally agrees to stop and with Dean's encouragement, lets the Trials go before collapsing.
After the collapse of Sam, Dean takes him to a hospital in Randolph, New York and desperately looks for a way to save him. In the end, he tricks Sam into allowing Gadreel to possess him to save him from the fatal damage the Trials did to him. After Gadreel turns on the Winchesters, kidnaps Sam and murders Kevin, Sam is left furious with Dean, partly because Dean talked him out of sealing Hell when he was almost done. This causes friction between them until Dean is killed fighting Metatron.
Despite Sam coming very close to turning him human, Crowley quickly reverts back into his old mannerisms, though he retains an addiction to human blood and some residual human mannerisms for the rest of the ninth season. After the end of the Trials, Dean chooses to keep him prisoner rather than kill him, seeing Crowley as a potentially valuable source of information. Following his need to enlist Crowley's help to save Sam from Gadreel, Dean lets Crowley go and Crowley forms an alliance with the Winchesters to fight Abaddon.
Following her defeat, Abaddon gets Jason to perform a ritual to restore Josie Sands' body for her use as a vessel once more and begins a crusade to rule Hell herself, the regime change she wanted to "discuss" with Crowley before Sam defeated her.
- First attempt at the Demon Curing Ritual. While it fails here, Sam is able to later successfully use it on a demon Dean in Soul Survivor though it isn't the exact same ritual he used on Crowley but rather a variation of it.
- While Josie's body is shown on fire, Sam apparently doesn't allow it to burn to ashes nor is it properly disposed of as Jason is able to gather her charred remains to restore for Abaddon to use as her vessel once more.