Appearances: Season 2
Four months prior to John Winchester's death, Ellen leaves a voicemail message on his phone, offering him help him with the demon. Sam finds the message and the boys travel to the Roadhouse. Ellen explains that she knew John and that he was "was like family once". While waiting for Ash to analyze John's information on the Yellow-Eyed Demon, Ellen offers the boys a case she was "saving for a friend".
After the boys kills the Rakshasa, they return to the Roadhouse where Ash has set up a computerized demon tracking system. Ellen invites the boys to stay, but they decline and return to Bobby's.
Ellen tries to prevent her daughter Jo from hunting on her own, but Jo sneaks off and joins Sam and Dean anyway. Despite getting Ash to help her cover her tracks, Ellen works out that Jo is in Philadelphia with the Winchesters. When she rings, Dean confesses that Jo has been kidnapped by the spirit of H.H. Holmes. Ellen flies out to Philadelphia, and after Jo is rescued returns back in the Impala with Sam, Dean and Jo.
Back at the Roadhouse, Ellen then reveals to Jo that her father was killed while hunting with John Winchester.
As he searches for the other Special Children, Sam seeks help at the Roadhouse. Ellen tells him that after they last met, Jo insisted on continuing hunting, and Ellen said "not under my roof". Ellen explains that she doesn't blame Sam and Dean for Jo leaving, or their father for what happened to her husband. She tells him she forgave John long ago, though she doubts he ever forgave himself. As Sam leaves, he asks Ellen to not tell Dean where he's going, and she reluctantly agrees. Sometime later, Dean calls her to check again if Sam had been there. She tells him, "Now, Dean, they say you can't protect your loved ones forever...but I say what the Hell. What's family for?" and sends him after his brother.
After the Roadhouse is suddenly and explosively destroyed by demons, Ellen turns up at Bobby's place. She explains that she was out buying pretzels when demons attacked the bar, killed everyone inside and burned it to the ground. But she also managed to rescue Ash's research from a safe that they kept there.
The Devil's Gate in Wyoming is opened. It is Ellen and Bobby who finally get it closed again. Afterwards, she leaves.
Appearances: Season 5
Ellen and Jo end up in a small town called River Pass in Colorado, and are there to help Rufus (a hunter and a friend of Bobby's) to get rid of the demons which have laid siege to the town. During the attacks, Ellen and Jo split up. Sam and Dean show up later and find Ellen, but Sam and Ellen appear to be possessed by demons from Dean's perspective. Sam is captured and tortured, and Dean and Ellen eventually arrive to his rescue. They later find Jo and Rufus and after a brief struggle, they convince Jo and Rufus that War, one of the four horsemen is responsible for making people see others as demons.
Jo and Ellen decide to help Sam and Castiel kill Lucifer. Castiel is eventually trapped in Holy Fire by Lucifer. The group continues into the town and is confronted by Meg and several Hellhounds. They escape into a store, but not before Jo gets mauled by a Hellhound. With desperation, Sam and Dean make a bomb and Ellen decides to stay with Jo, saying someone needs to open the door. Jo and Dean share their first and last kiss before the Brothers leave. Eventually, Jo dies in her mother's arms and Ellen is left to blow up the building.
Appearances: Season 6
Ellen shows up as Bobby's wife. Due to Balthazar changing events in the past, Ellen is back along with Jo and 50,000 other random people. These events didn’t last when Balthazar set history right and sank the Titanic again.