Following the release of Lucifer, the Winchesters began looking for a way to defeat him and the Prophet Chuck passed a message through Becky Rosen that the angels had lost the Michael Sword and that it was in a castle on a hill made out of 42 dogs. Looking to find the Michael Sword for herself and her father, Meg had a demon possess Bobby Singer to get close to the Winchesters who didn't realize he was possessed. During that time, the demon tried to cause problems between the Winchesters and the real Bobby by telling Sam to lose "his" number for starting the Apocalypse.
Dean eventually figured out that the message referred to John's Lock-Up at Castle Storage at which point Bobby revealed himself to be possessed and attacked Dean. As the demon restrained Dean, Meg arrived with a minion and was amused by the fact that Dean was the one who was supposed to kill Lucifer. She reveals that she knows the Winchesters and Dean at first thinks she's Ruby, but Meg tells him to think further back and he realizes that she's Meg. Meg gives the demon in Bobby the demon-killing knife to kill Dean, but Bobby fights for control and eventually manages to regain control long enough to stab himself in the gut with the knife, killing the demon and leaving him seriously wounded. As Sam returns, Dean engages Meg's demon minion and Sam fights Meg. Neither Sam nor Dean are able to beat their opponents at first, but Dean finally kicks the demon minion's feet out from under him, grabs the knife from Bobby's gut and kills the demon before he can recover. Dean then advances on Meg who quickly smokes out of her vessel and flees.
Sam and Dean rush Bobby to the hospital and then, knowing that the demons know the location of the Michael Sword, rush to John's Lock-Up where they find that Zachariah and his men killed the demons that got sent there. They then learn that Dean is the Michael Sword, or rather his true vessel and while Zachariah tries to torture a "yes" out of Dean, the return of Castiel stops him.
Bobby survives his wounds, but is left paralyzed from the waist down. He tells Sam that it was the demon that was talking when he told Sam to lose his number and he wasn't cutting Sam out of his life. Due to becoming a Fallen Angel as a result of his rebellion, Castiel is unable to heal Bobby's injuries when they ask him to. Bobby's paralysis is later healed by Crowley using a crossroads deal the two make. Sam later asks for his advice when he considers saying Yes to Lucifer to cast him back into the Cage, but Bobby tells him he was fighting a low-level demon and only regained control for a moment while Sam would be fighting a very powerful archangel.