Sam and Dean are finally reunited with their father. But happy endings aren't in their family's future. John tells them about "The Colt", a gun that can kill anything. And right now it's in the wrong hands.
In a surprise ending, Jake stabs Sam and kills him. Devastated by grief, Dean makes a deal with the crossroad demon to bring Sam back; as a trade-off, Dean gets one more year to live, after that -- his soul is toast.
Following what Sam has seen as a vision, Sam and Dean visit their childhood home in Lawrence Kansas. Sam and Dean discover an unseen force is terrorizing the current residents of their house, a mother and her two children.
Sam and Dean are investigating a series of strange accidents on a mountain road when they come across Molly, who insists she and her husband just crashed their car, but her husband and car are missing.
A spate of wild dog attacks draws Sam and Dean's attention. Sam and Dean suspect that it has something to do with a werewolf. They visit Madison, a friend of one of the victims thinking she may be the next victim.
Drawn to a town lighting up with demonic signs, John meets Lily, a girl whose mother died in a fire years ago much like the one that killed Mary. John learns Lily has a fatal gift; if she touches someone they die.
Dean wakes up one day in a totally different world. His mother Mary is alive, he is married to a fine woman, and Sam is engaged to Jessica. Dean soon realizes he's been captured by a Djinn, who is slowly bleeding him dry.
While driving through New Orleans, the Winchester boys are stopped by the police and arrested. It seems there have been a series of accidents caused by an Impala and the police think they're the perps.
Sam and Dean investigate a serial murder case and learn that since the 1960's similar murders have been repeated every 15 years. They meet Dr. Richard, the widower and Richard's young and beautiful second wife, Michelle. More attacks occur.
An architect commits suicide. Sam and Dean followed a clue that some other successful people had died in the similar way as the architect within a year, and find out that those people had all bargained with "the crossroad demon".
In Afghanistan, Jake, a foot soldier was always being made fun of. However, when the troops faced destruction, he exercised his superpower to help his fellow soldiers and evacuated them from the battlefield. Meanwhile, Sam sees another premonition.
Dean visited Missouri because he struggled with the true meaning of John's last words... "Save Sam, or kill him". Some old photos remind Dean of Mrs. Lyle, who was Sam's teacher. He remembers how he and his father saved Sam, despite what his future held.
In a small town in Colorado, Sam and Dean investigate a series of cattle mutilations, the beasts have been drained of their blood. They run across Jason, a hunter who specializes in vampires, but wonder why he's in town.
Part 1 of 2. In the second-season finale, Sam is abducted by the Yellow-Eyed Demon and taken to a ghost town with others who have special abilities. The Demon intends to initiate war against the human race, and he tries to get Sam to join the fight by showing him what happened to one of his parents.