[[12.03 The Foundry]] begins with [[Mary]] finding a case in Minnesota where people are found dead after reporting hearing a baby crying. [[Sam]] expresses concern over Mary's desire to get back into hunting but [[Dean]] is all for a "family hunting trip". Mary struggles with her lack of knowledge about the technological methods the boys use and the aftereffects of the attack. While salting and burning what they think is the ghost's bones, Sam remains concerned about Mary but Dean still believes she's just "adjusting". They return to the room to find Mary gone and upon discovering she's returned to the house, they return to rescue her but she's been possessed by the actual ghost. The ghost tries to make her kill Dean but she resists it and releases him. Dean keeps the ghost occupied while Sam finds the bones and burns them, which releases Mary and the ghosts of all the children in the house. Back in the Bunker, Dean apologies for taking over her case, but becomes hurt and angry when Mary says she has to leave to have some time by herself.
In [[12.04 American Nightmare]] Dean, still upset about [[Mary]]'s departure, travels with [[Sam]] to Mason City, Iowa, to investigate a person who died while being flayed by an invisible force and displaying signs of stigmata. As they discuss the victim, Olivia, with the priest who witnessed her death, Sam notices Dean is very short with him. They wonder if perhaps it was caused by a rogue angel, so Dean calls [[Cas]] to discuss the case. After hanging up with Cas, Dean texts Mary to check in on her and asks if he should still call her Mom. Sam returns and Dean briefs him on Cas' news -- the gates of Heaven are still closed, so it can't be an angel, and he and [[Crowley]] have teamed up to hunt for Lucifer, who has possessed the "Master of Butt-rock" [[Vince Vincente]]. Dean teases Sam when he defends Vince. They head to the morgue to examine Olivia's body, where Dean is dismissive to the medical examiner, and when Sam calls him out for being cranky, Dean denies it. They question Olivia's former employee and replacement, Beth, who's also a Wiccan, which causes Dean to believe she is responsible, but Sam disagrees. A grocery delivery guy is killed in the same fashion, and Olivia's case files show a connection to the Petersons, a "real Old-Testament type" family. They question the family, and afterward, Sam once again questions Dean about Mary's departure and how he's dealing with it, which Dean again brushes off. Discussing the case, Sam believes the ghost of their dead daughter, [[Magda]], is responsible. Dean disagrees, believing Beth is the killer and leaves to track her down, leaving Sam at the farm. Dean questions Beth and determines she was not responsible for Olivia's death. He receives a phone call from Sam who tells him Magda is still alive before he is attacked and the phone disconnects. Dean rushes back to the farm in time to save Sam, who was about to be poisoned by the Petersons. Afterward, Dean receives a text from Mary where she apologizes for not getting back to him sooner and says that she will ''always'' be "Mom".
[[12.05 The One You've Been Waiting For]] finds [[Sam]] and Dean in Columbus, Ohio, to investigate a case of two people falling victim to apparent spontaneous combustion. While investigating the shop where the deaths occurred, Dean finds a hidden room full of Nazi paraphernalia. Meanwhile, Sam hacks into the shop's computer and discovers the victims were meeting regarding an antique pocket watch, and that the store owner had a whole business catering to "Nazi nutjobs". He finds out that the pocket watch used to belong to Hitler's inner circle, and the boys presume the [[Thule]] are involved. They call [[Aaron Bass]] to see what the [[Judah Initiative]] knows about any local Thule activity. Aaron tells them they've all come back to Germany regarding a mission called "Das Blut" (The Blood). They ask him about the pocket watch but he doesn't know anything. When news of another spontaneous combustion death pops up, they head to the crime scene -- the apartment of a young woman who managed to escape. They leave the apartment in time to see a cop car driving off, with a woman in the back screaming for help. The follow the cop car to a parking garage where they rescue the woman, [[Ellie]], and tie up her captor for questioning. He is [[Christoph Nauhaus]], the son of [[Commandant Nauhaus]], a ranking officer in the Thule High Command. He explains how the soul of [[Hitler]] is trapped in the pocket watch "like a Horcrux", and the Thule plan to use it to resurrect Hitler, along with Ellie's blood, because she happens to be a direct descendant of Hitler -- "Das Blut". The boys convince Ellie to help them set a trap for the Thule, but while fighting Thule thugs, Ellie jumps out of the window and is captured by Nauhaus and Christoph. The boys head to a diner to research a tracking spell to find her, when Christoph arrives, having overheard their location while escaping execution. Christoph leads them to the location where the resurrection ritual is taking place. Handcuffing Christoph in the Impala, they plan their attack. Dean wants to use the [[Grenade Launcher]] but Sam refuses since they need to be stealthy; he promises Dean he'll be able to use it someday. The boys launch their attack but are captured and brought to the room where Hitler's soul has already been transferred into Nauhaus. Ellie is lying on a gurney, weak from blood loss. she staggers from the gurney, grabbing a gun and shooting one of Nauhaus/Hitler's flunkies. Dean uses the distraction to grab a gun and shoots the other flunkies, then shoots Hitler. They walk back to the Impala with Ellie, and Dean exclaims multiple times "I killed Hitler!". They release Christoph and take Ellie back to her apartment. Dean suggests heading for pie since he deserves it after... killing Hitler!