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Callie convinced House to treat her as an adult so he wouldn't report her to child services. However, his team grew suspicious and Adams finally got the opportunity to report to child services that there was an unaccompanied minor in the hospital.
Finally, Ellen showed up, and was immediately rejected by her daughter. When Adams inquired why, Callie told her that Ellen had abused her.
However, House confronted Ellen. Ellen admitted she had been an alcoholic and that's why Callie ran away. She had also been sober since Callie left.
When Adams asked Callie why she lied about her mother, Callie responded that people don't understand it when your parent is an alcoholic, but they will understand if you tell them it was physical abuse.
As Ellen became Callie's medical proxy, she got to make all of Callie's medical decisions, and they often fought over the course of Callie's treatment. House believed that Ellen was doing more harm than good and that she would most likely crack under stress. He went to her and told her that Callie would be better off without her, then "accidentally" left behind his Vicodin to tempt her. Not only did Ellen not fall for the bait, she chose the course of treatment House disagreed with.
As the treatment progressed, Callie and Ellen started to talk through some issues. Eventually, the doctors found the correct diagnosis and Callie started to improve.
However, when Ellen came back to Callie's room, Callie had run away again. She was too afraid that her mother would relapse and wanted to remember her the way she was.