Sam collapses as Season 9 begins and Dean sends out an emergency plea via prayer to every angel in the area to help Sam. In exchange, Dean agrees to owe that angel a favor. But his request is answered by numerous angry angels who want to kill him. Meanwhile, Castiel struggles to survive without his powers.
Sam and Dean meet Dorothy from Oz and the wicked witch when they locate an ancient computer in the Men of Letters house that dislodges a hidden hex bag that in turn unleashes a magical green-webbed wall. Dorothy became trapped in the web years ago to stop the witch from finding the key that would open the gate that connected their world to Oz.
Sam and Dean investigate two gruesome murders and realize that a German shepherd witnessed both deaths, so they use a spell that allows Dean to communicate with the dog. Unfortunately, the spell comes with unexpected side effects.
Castiel gets a job and starts enjoying life as a human, but when he learns about some local disappearances he asks Dean to help him investigate. Meanwhile, Crowley agrees to help decipher the tablet in return for one phone call to hell.
Dean helps an old friend with a ghost problem at a home for delinquent boys. Dean was sent there years before for stealing food. When Sam learns about Dean's past he is stunned and asks for more information, which Dean is reluctant to give.
Sheriff Mills asks Sam and Dean to help her investigate the murders of four members of a church chastity group. Dean disappears shortly after the brothers join the group; and Sam and the sheriff team up to rescue him.
An angel war begins and a massive amount of angels are slaughtered. Sam and Dean investigate and run into Castiel who is soon captured and tortured. Meanwhile, Dean questions Ezekiel's demands and wonders if it is time to tell Sam the truth.
Crowley, who wants to reclaim his place as king of hell, seeks Dean's help to find the "First Blade," the only blade that can kill Abbadon. Unfortunately, Cain, the first-born son, controls it. Meanwhile, Castiel tries to extract some grace from Sam to track Gadreel.
Sam and Dean work undercover at a spa to investigate murders in which the victims were hundreds of pounds lighter after their deaths. All of the victims attended the spa for weight loss; and the brothers suspect that witches are to blame.
Sam and Dean are shocked to discover that the Men of Letters' bunker is haunted. Their investigation leads them to a storage facility where the demons are keeping a prize possession. Meanwhile, Castiel is captured by Bartholomew.
Sam and Dean get help from a former member of the Men of Letters to locate the First Blade, after Crowley falls off the wagon and starts injecting himself with human blood. To make matters worse, a demon betrays Crowley and tells Abaddon that the Winchesters are searching for the First Blade.
Sam visits a town where ordinary people are turning into violent murderers. His investigation reveals that the Men of Letters came to the town in 1958. Meanwhile, Dean struggles with effects from the Mark of Cain and is tested by Crowley.
Sam and Dean look into monster families that are running Chicago's underbelly, including a clan of shape-shifters and a group of werewolves. Meanwhile, they meet someone who holds a personal grudge against the creatures.
Abaddon demands that Crowley help her kill Sam and Dean. When he refuses, she reveals a shocking bargaining chip to change his mind. Meanwhile, Castiel captures one of Metatron's angels, and gets Sam and Dean to help him with the interrogation.
Tessa the Reaper returns and leads a conspiracy against Castiel's angel followers. Meanwhile, Dean is eager to use the First Blade when the angels are attacked, but Sam worries about the cost to his brother whenever he uses it.