|At the beginning of season two, the trio are rescued via MEDEVAC and taken to the hospital, but due to his extended injures caused by both the demon's torture and the car accident, Dean is comatose. John summons the demon to make a deal and trades the gun and his own life for Dean's.|
Both Dean and Sam struggle to cope with John's death while trying to continue their job. As they continue to hunt any supernatural spirit they find, they come across many people that share the same story as Sam, a mother who mysteriously dies in their nurseries when the children were 6 months old. These "special children" each discovered recently that they have some sort of psychic power. In the light of these revelations, Dean reveals to Sam that their father (just before giving his life to the demon) had told Dean he had to save Sam or be forced to kill him. Various revelations occur throughout the rest of the season that lead the pair to believe these psychics are being trained to participate in an army that the demon will lead in a coming apocalypse.
After several months of "by-the-book" jobs, Sam disappears while ordering food at a diner. He awakens in a ghost town with four other psychics, two of whom he had met in prior episodes (Ava from Hunted and Andy from Simon Said). There, in a dream, the demon reveals to Sam he has brought all of them to the town to compete against one another and the winner (the only one left alive) would become the leader of the demon's army. The two innocent psychics are killed, before Ava (who has killed Andy by summoning a murderous demon) is revealed to be a demonic familiar herself. Jake, an Army soldier who claims he was abducted from Afghanistan, kills Ava by snapping her neck after taking her by surprise. Dean has been frantically trying to locate his brother, discovering the Roadhouse has been burned to the ground, leaving Ash dead and Ellen missing. With the help of Andy, who can "beam information" directly into people's brains, Bobby discerns where Sam and the others are (a haunted ghost town in rural, fictional "Cold Oak, South Dakota"). Upon their arrival, Dean and Bobby watch in horror as Sam is stabbed in the back by the only other survivor, Jake. Sam dies in Dean's arms.
In the season finale, Dean, distraught and unable to cope with the loss of his brother, believes that he has let Sam down. His mind made up, Dean sets off without Bobby, leaving Sam's body behind. He makes a deal with the demon at the crossroads, his soul for Sam's. The demon agrees and brings Sam back from the dead. However, she tells Dean that she will only give him one more year to live, and if he tries in any way to prevent his death, Sam will drop dead on the spot. When Dean returns, he finds his brother alive and well and unaware of all that has happened. After everything Dean went through knowing that his father had died for him, he wants to protect Sam and decides not to tell his brother that Jake had killed him.
Ellen, who was away when the roadhouse burned down, finds Bobby, Dean, and Sam and shows them a map that Ash had prepared just before his death. They discover that an elaborate gate was constructed by Samuel Colt to bar an entrance from hell. The demon tells Jake that he must open the gate and that the Colt is the key. The whole group arrives to stop Jake, who is beyond surprised to see Sam and insists that he killed him. Jake gets the gate open but is shot to death by Sam.
The demon returns and taunts Dean with the possibility that the Sam that Dean has had resurrected, may not be "one hundred percent pure Sam." He then attempts to kill Dean. However, John Winchester, who has escaped from hell, manages to save his son. Dean shoots and kills the demon with the last remaining bullet in the Colt, and John's soul departs, no longer condemned to hell. Bobby and Ellen are able to close the gate, but not before hundreds of souls and demons escape. Sam is suspicious and wants to know why Jake insisted that he had killed him. Dean is then forced to reveal the deal he had made at the crossroads, and Sam, who is upset over the sacrifice Dean has made, promises to save him.