|“||John was like family once||”|
— Ellen to Dean
in Everybody Loves a Clown
Ellen and her husband were once very close friends with Dean's father, John. However, once her husband was killed because of a mistake John made on a hunt together, John couldn't bring himself to look Ellen in the eye anymore. Ellen says that she forgave John for what happened to Bill, but she didn't know if he ever forgave himself. They had not spoken for a very long time before his death, but she did leave a message on his cell phone offering to help with the Demon, which is how Dean found her.
|“||Well Dean they say you can't protect your family forever. Well I say screw that.||”|
— Ellen to Dean
Sam and Dean go to the Roadhouse again in "Simon Said" to have Ash help them track down one of the Special Children. After the case, Dean gets a call from Ellen telling them to return to the Roadhouse. She asks them to tell her about their last case. Dean initially does not want her to know but she convinces them saying "...the best we got is us, together. No secrets or half-truths here." After learning the truth about the Special Children, she has Jo break out the whiskey.
Ellen and Dean's relationship is strained in "No Exit". Sam and Dean walk into the Roadhouse to witness a fight between Ellen and Jo about Jo hunting. Jo shows them the research she has done and Ellen tells them they should take the case, which they do. Against Ellen's wishes, Jo sneaks away and follows them. When Ellen calls to see if Jo is with them, Dean lies to her on Jo's request, which he feels bad about. However, she finds out from Ash where Jo really is and calls Dean again, furious that she lied to him. When she finds out Jo has been kidnapped by a ghost, she get's on the first plane out. After Sam and Dean save Jo, they all ride back in the Impala together. Ellen doesn't say a word and turns off the radio when Dean turns it on. When they get back to the Roadhouse, Dean apologizes to Ellen and leaves. Ellen the reveals to Jo that John is the reason her dad died.
When Sam leaves Dean in "Hunted", Dean phones Ellen asking if she has seen him, which she hasn't. However, Sam does eventually come to the Roadhouse to track down the other Special Children and Ellen reveals that Jo left to continue hunting, but she doesn't blame the boys. Even though she tells Sam that she won't, she phones Dean to tell him where Sam is. She also reveals that she doesn't hate Sam and Dean for what their father did and that she long ago forgave him, but that John could never forgive himself.
Dean phones Ellen again in "Born Under A Bad Sign" to see if she has seen Sam, but she hasn't this time.In "All Hell Breaks Loose - Part 2" Ellen interrupts a conversation between Dean and Bobby in the salvage yard and hugs Dean. She reveals that when demons burned down the Roadhouse she was out buying pretzels, but Ash and everyone else inside had died. She tells them that she got Ash's research out of the safe, and they all discover the Devil's Gate in Wyoming. At the gate, Jake Talley has Ellen put her gun to her head, but Dean and Bobby pull it up before she shoots, while Sam kills Jake. Ellen and Bobby are the ones who close the Devil's Gate. Afterwards, she tells Sam and Dean that although the Yellow-Eyed-Demon was dead, a lot more demons got out through the gate.
|“||You can't pick up a phone? What are you, allergic to giving me piece of mind?||”|
in Good God, Y'all
After closing the Devil's Gate, Sam and Dean seem to lose touch with Ellen, which greatly upsets her.
|“||I said go. And Dean? Kick it in the ass. Don't miss.||”|
— Ellen's last words to Dean
in Abandon All Hope...
In "Abandon All Hope...", Ellen and Jo help the brothers again in their mission to kill the devil. The night before, they take a group picture at Bobby's house. Once at the town, Dean tells Ellen, Jo and Castiel to look around while he and Sam check out the police department. After Castiel goes of by himself and is kidnapped by Lucifer, Ellen, Jo, Sam and Dean regroup. They are confronted by Meg and several Hellhounds who tells them her father wants to see them and that they can make it easy or really really hard. Dean looks to Ellen for approval, and she nods. Dean shoots a Hellhound and the group starts running. Dean is knocked down, but is saved by Jo, who is then attacked and fatally injured by the Hellhound. They go into a store and block all the entrances so the hounds can't get in. Jo tells them that they need to be realistic and that she isn't moving, but she can still do something: she wants to build a bomb to kill the Hellhounds and stay behind to blow it up. The group doesn't like it, but they know it is the only option, so they do it. Once the bomb is made, Ellen announces she is staying behind with Jo. Sam and Dean are upset, but they respect her wishes. She tells Dean not to miss and then they leave the building. Ellen let's in the dogs and then sits next to Jo and blows up the building, killing herself and the Hellhounds.
Ellen has been mentioned many times since her death by Dean, as it affected him greatly.
Ellen tries to reach to Dean from the other side (via a psychic) to tell him to trust someone again, and not to hold it all in, threatening to kick his ass if he doesn't do it. Even in death, Ellen worries for Dean. Upon hearing this, Dean decides to tell Sam what is going on with him.
In an alternate reality created by Balthazar un-sinking the Titanic, Ellen is still alive and is married to Bobby. Dean phones her about the case he is working and she co-ordinates between him and Sam and Jo's group of Hunters. However, when the timeline is reverted, Ellen is gone again.