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First, Mulder died. Not like in New Mexico or in Montana. He just died, old, withered away.
She thought she was broken but she had no idea. It was enough to not really enjoy the remaining time with Jackson or Lily, but in the long term that didn't matter either. She ate and she drank and she shat and she pissed and she couldn't find joy in any of it and after some centuries she thought this was the way it had to be. She still talked to people far and in between. And then there were no people anymore. She may have been alive for three millenia or twelve, it didn't matter in the end.
She was alone. The last human being. The world changed vastly around her, mammals lost the fight. She lost hers too, over and over again. She had tried every single version of killing herself.
At first, it was out of pure desperation, then it felt more like a lover's touch. Wandering around the wasteland, finding a knife which she just knew had been touched by another human being, even if it was centuries ago.
Later she even found consolation in the kissing lips of a volcano and she drowned every other day. Everything was better than just being around. She starved, she froze, she was attacked, but it was never enough.
Everything was loud but she never heard anything. She lost her sense of speech, then her sense of thought but she didn't realize the bliss until later.
When the sun blew up five billion years after that everything around her died. She had been long over being interested in anything, but now hell really started.
The planet was still intact, as in round and spinning, but over some millennia she was not only alone but the last living creature at all. Then the hull began to dissolve and she died every single second just to be awake in the next. Swimming in lava for billions and billions of years. Her mind was gone after that but her body was still going.
The sun got small and cold, she did also. She hadn't moved a muscle for millions of years and she wouldn't start again. She froze every single second just to be awake in the next. Every now and then her brain did something, sending her a picture of her children or her love, an animal or a plant, the ocean, a color but she was not there to receive the message. She just was.
Then the sun went out completely. Scully was still around. One after one, every star blew off, and after 10¹⁴ years - which were still a thing, since her dead rock spun still around the cold center mass - everything was cold and dark and she was the last thing alive in the whole universe.