In Oregon, a couple is flying a plane in the middle of a storm, and the woman, Penny Dessertine, looks out the window. She sees something huge fly by, but her boyfriend Stan doesn't see it. He promises there's nothing out there and tells her to lean back and try to relax. She closes her eyes, but something rips Stan out of the cockpit window. Penny screams in horror as the plane goes down.
Castiel emerges from Bobby's safe room and tells Dean that Sam's soul is in place. However, he doesn't know when or if Sam will wake up. Castiel tells Dean that Sam's soul is in agony, just as he warned Dean, and says Dean should have just killed Sam outright. The angel disappears and Dean shares a drink with Bobby. Bobby insists that Sam will bounce back, but Dean isn't convinced. They discuss a case that Bobby is working, about a plane crash. The pilot was discovered 17 miles away from the crash, and the woman has disappeared without a trace. Sam staggers in and hugs Dean. However, they realize that Sam doesn't remember anything from the moment that he fell into the cage with Lucifer and Michael.
As Sam eats, Dean confirms what his brother remembers, and then tells him that he's lost the last year and a half of his memories. Sam asks what Dean did, and Dean explains that he made a deal with Death. Bobby doesn't believe that they've got away with it neat and clean, but Dean insists that they have and refuses to tell Sam what he's done since then.
Later, Dean talks to Bobby privately, and Bobby admits that he still has misgivings given that the soul-less Sam tried to kill him ten days ago. Dean says that they can't tell Sam the truth and risk breaking the mental barriers that Death created, but Bobby warns that Sam will eventually learn the truth. He agrees not to tell Sam, but warns Dean that it won't be pretty when Sam finds out.
Dean and Bobby prepare to go to investigate the plane crash, leaving Sam behind. However, Sam wakes up and insists on going. Bobby tells them to go on without him, raising Sam's suspicions. Dean assures him that it's just Bobby being cranky.
As the brothers arrive in Oregon, Sam confirms that two other girls have vanished and there's no connection between them and the plane crash victim. Sam then asks if Dean tried to live a normal life, and points out that Dean is exactly the same. Dean admits that he was with Lisa and Ben for a year, but all he'll say is that it didn't work out.
Sam and Dean talk to Penny's sister, Sss, who explains that Penny only went up in the plane because of Stan, her boyfriend. Back at the motel, Sam confirms that the first two girls were involved in church work, but Penny wasn't a Christian. Dean reveals that he stole Penny's diary, and confirms that Penny was a virgin.
At the local college, Melissa says goodbye to her friends and walks across campus on her own. She looks up at the sky as something descends toward her, and then she runs away in horror but trips as her pursuer closes in.
The next day, the brothers visit Melissa in the hospital. She explains that her attacker looked like a giant bat, and grabbed her by the shoulder. She passed out and it was gone when she woke up. Melissa says that her golden promise ring was stolen, and Dean asks if she's really a virgin. Melissa finally admits that the boy she did have sex with didn't count. Back at the motel, the brothers try to figure out what is interested in virgins and gold. Sam ends up at World of Warcraft websites, and they all talk about dragon. Dean admits that it's been possible and calls Bobby for a second opinion. He insists that dragons aren't real, but agrees to check around.
As the brothers go over their files, Sam wonders if they took on a skinwalker recently. Dean insists that they haven't, but Sam isn't convinced. Bobby calls back and refers Dean to a Dr. Visyak, an expert on medieval studies at San Francisco University.
In the underground tunnels beneath the town, the captured women are locked up. A dragon arrives, transforming into human form, and drops off a new captive. He breaks her arm when she resists and tosses her in with the others. The dragon then generates head from his bare hands, welding the cage door shut.
Dean arrives at Dr. Visyak's home, but she only lets him in when he mentions Bobby's name. She tells Dean to kick Bobby in the groin the next time that Dean sees him, but says that Bobby will have to explain it. Dean asks her about dragons and Dr. Visyak explains that it's been 700 years since dragons were last seen. The only way to kill a dragon is to use a blade forged with dragon's blood, and there are only a few left. She finally tells Dean that she has one in the basement, and shows it to him. It's bound into a stone to protect it, and only a brave knight can pull it free. Dean grasps the hilt and pulls, but nothing happens except that Dean strains something. However, he has another idea, but warns Dr. Visyak that she won't like it.
At the motel, Sam calls Bobby and asks for helping figuring out where the dragon lairs up. There are no caves, so Bobby tells him to consider alternatives. Sam figures the creature is hiding in the sewers and thanks Bobby, and then asks if he's okay. Bobby insists that nothing is wrong, and nothing happened in the last year and a half that involves Sam. He quickly hangs up, and Sam tries to summon Castiel. The angel appears, unaware that Dean and Bobby are hiding the truth from Sam. Castiel asks how having soul back feels, and Sam plays along, saying he's fine. He asks for more detail and the angel helps out.
Dean prepares to blast the stone open with plastic explosives, ignoring Dr. Visyak's objections. She reluctantly gives in since they have no other choice. Dean sets the charge and backs away, and then hits the detonator. The plan works, and Dean pulls the sword out... only to discover that he's blown it apart.
Later, Dean meets with Sam and shows him what's left of the blade. Sam has pinpointed the dragon's location in the sewers and Dean prepares to leave. However, he notices Sam hesitating, but Sam says it's nothing.
In the sewers, the brothers find a pile of gold jewelry and realize they're on the right track. Sam finds a table with candles and a journal on it. They hear women yelling and go to investigate. The women warn the brothers that the dragon is coming back. The dragon in human form attacks them, stunning Sam. Dean manages to cut him with the blade, but the dragon knocks it out of his hand. Dean goes for the blade while Sam tries to hold the dragon, off, but a second dragon attacks them. Sam manages to stab the newcomer with the sword shard, killing it, and the first one escapes.
Later at Bobby's, Dean is gloating over the gold that he took. Sam apologizes, and insists that Dean should have told him. He feels that he should make amends, pointing out that it was still a part of him that did everything, and asks Dean what he did. Dean warns how dangerous it is, but Sam points out that Dean would do the same thing. Bobby calls them in and explains that he's been translating the dragon's journal, which is written on human skin. The book describes a place of blood and bone, filled with the souls of all the monsters.
The second dragon meets another of its kind, who says that it has enough virgins to meet their need. They open the van and take out one of the virgins, and drag her to a nearby cave.
Bobby explains that the book describes Purgatory, and it contains instructions on how to open a doorway there. The page with the specific instructions is missing.
The dragons take the virgin to the edge of a vast chasm and read an inscription from the missing page. A huge fire ignites below, and one of the dragons cuts his arm and lets the blood drip down. They then throw the virgin in and finish the incantation.
Bobby warns that the book explains that the ritual can bring something from Purgatory, but he doesn't know what. All he has is a name: Mother of All.
The dragons look on as a female emerges from the chasm, her eyes glowing. They greet her, and she tells them that they have much to do and it's time to get started.