She was later resurrected after thirty years by the Darkness and reunited with her now grown sons. She later died three years later, but reunited with John in Heaven.
Mary was a hunter along with her family. She began dating John Winchester in the 1970s. Her parents were murdered, and Mary ended up making a deal with the yellow eyed demon Azazel in order for John to be brought back for the dead, with the deal being that Azazel will call upon her future child's room when the time is ready.
In the prologue taking place in 1983, Mary comes across Azazel in her baby son Sam's room. When she tries to intervene, the demon pins her to the ceiling and sets her on fire, which is witnessed by her husband John. John escapes the burning house with their two sons Sam and Dean. The incident leads to John becoming a hunter of supernatural beings and brings up their sons to follow the same path, with the goal being to find the thing that killed her. It isn't until 2006 when they find out that Azazel is involved.
Dean ends up going back in time and meets younger versions of his parents, in which he discovers that Mary was once a hunter. The events are witnessed in which she makes a deal with Azazel to spare John, in exchange for Azazel visiting her family household at some point in the future.
Dean and Sam end up going back in time, which is a few years following the time frame seen in season 4. Mary and John are married at this point and settled into family life. The angel Anna travels back in time to try and kill Mary and John in order to stop Sam and Dean being born so the apocalypse (which began in 2009) wouldn't happen. However the archangel Michael possesses John and kills Anna to stop her changing events, and proceeds to wipe John and Mary's memories so they wouldn't remember the incident. This devastates Dean, as he had previously warned Mary not to enter Sam's bedroom in 1983, meaning her fate was sealed and that she would end up dying.
After helping the Darkness reconcile with her brother God, the latter promised Dean she'd repay him by giving him back something he wanted. Dean later discovered that the Darkness had resurrected Mary as a thank-you gift.
After her resurrection, Mary reunites with her son Dean and sees the new world after thirty years. Mary is out of place in it but continues to be a hunter with Dean and Sam. She also befriends the angel Castiel who relates to being out of place and she comes to see him as family after he saves her from the reaper Billie.
Mary finds it hard for her to adjust in being in a new era, due to the unbelievable things that have developed. She leaves her sons to find herself and adapt to the new ways of civilization, though she keeps in contact with Dean after he calls her.
Mary joins the Men of Letters who trained her already skilled hunting expertise and help her with adapting to technology. Mary also helps Sam in defeating the Alpha Vampire.
Mary was left stranded with Lucifer in the other universe and wandered the other world facing problems such as crazed hunters or angels attacking her but Lucifer saved her from the threats. However, they were confronted by Michael who promptly defeated Lucifer after learning they were from another reality.
While mastering his powers, Jack searched for other realms to find Mary for her sons as he wanted to rescue her in order to prove he is good. Jack's search led him to find Dreamwalkers, people who can see other worlds and he found the world she was in.
Jack was found by Sam and Dean, who he told of his plans before letting them see the vision of the world Mary was trapped in. Mary was shown in a cage being tortured by spikes stabbing her repeatedly as she called out for help. This display caused her sons to finally learn she was still alive.
After finding a more stronger dreamwalker and bonding their powers to create a rift, Jack was accidentally sent to the world that Mary was in as she was confused by his presence and identity.
In Good Intentions, Mary was taken out of her cage and was placed in a cell before Michael tosses Jack in it. She learns he is the Nephilim that Kelly Kline was carrying who rapidly aged himself and he tells her that her sons sent him to rescue her. She asks about them and is relieved they aren't present in Apocalypse World and she tells Jack to let Michael kill her since they can't allow him to invade Earth but Jack wanted to rescue her. They escaped when they learn the fortress has a spot of weak warding and the two meet the Alternate Bobby and go to his colony.
Mary helps a survivor before she is confronted by Zachariah who overpowers her and demands Jack's location. She insults him and he moves to kill her but Jack returns and kills the angel in front of Mary and Bobby who just arrived. Mary then saw Jack kill three more angels who were coming.
In Bring em' Back Alive it was mentioned by Charlie Bradbury that Mary and Jack have formed a resistance against Michael.
During Funeralia, Mary and Jack see many victories over Michael's forces but mary is concerned about the survivors they are taking in. She has come to see Jack as family and act as a guiding figure to him.
In Beat the Devil, Mary and her group detect intruders and investigate before she reunites with Dean and Castiel while meeting Gabriel. She hugs Dean and asks him about Sam though Dean's facial reaction tells her his fate and she is devastated. When Dean decides to retrieve Sam's body, the camp bell rings and Sam arrives alive and smiles at his mother before she sees him being followed by Lucifer whose arrival shocks her.
Castiel tells Sam and Dean that he visited Heaven, and discovered that John and Mary are living together in their own personal heaven.