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This article is about a character appearing in the animated series, which is not canon. You may be looking for the live-action series counterpart, if any.
After her death, Mary continued to haunt the old Winchester home. She initially took the form of a fiery being (possibly depicting the way she was killed).
In Home, Sam had premonitions of a woman crying out for help at his old home. Reluctantly, Dean agreed to investigate it. With the help of Missouri Mosely, they concluded that two ghosts had been haunting their home. When they kept a vigil at the house, things started to get worse and a fire broke out. Though they managed to get the new tenants to safety, Sam was trapped by a malevolent spirit who tried to strangle him using chains.
The fiery entity returned, and instead of harming Sam, freed him from the clutches of the spirit. The fiery being was then revealed to be none other than their long deceased mother. She had a final conversation with them, saying how proud she was of Dean. She then left the house and managed to drive the other ghost out too.
Mary appeared again in What Is And What Should Never Be, as part of the fantasy world conjured by a Jinn for Dean, so it could drain him of his life force. This Mary was unaware of the fire that destroyed their home and instead enjoyed a happy birthday celebration with her two sons and daughter-in-law, Carmen Winchester. She met Jessica during the celebration, and was happy to hear Sam was engaged to her. Mary was also a widow, due to the death of John a year prior. Dean ultimately chose to leave the fantasy world in favor of his hunting lifestyle in the real world.