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so when scully comes to her house after mulder told her that scully's gone missing & they aren't exactly sure what happened, and scully is ranting to her about mulder deceiving her and abducting her and putting a chip in her neck — she tried to deal with it on her own, talk her daughter down until mulder wouldn't let her do it alone. she stands in front of mulder to stop her daughter who she knows is not in her right mind. she's protecting mulder, but so much more than that she's protecting scully, the only daughter she has left who rarely turns to her mother for anything, who keeps her own counsel and only came to her twice in the last year. both times because of mulder. maggie scully is under no illusions of what's between her daughter & mulder, and she knows how important scully's job & partnership are to her regardless. maggie can imagine how the weight of killing or hurting mulder would destroy scully. she already shot him to protect him, and i think that was incredibly hard for her to do.