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She smiled fondly at the man currently sleeping on her sofa. Yes, he was an absolute terror to live with, but he was truly a good man, deserving of her affection. He had said horrible, stupid things to her in the past, but with his revelation, You've always mattered, she knew that he had always cared for her. Yes, he had played with her feelings a bit, flirted to get what he wanted, but sometimes, buried deep in the rubble of his worst moments, there were shining little pieces of genuine kindness waiting to be unearthed.
Like the way he had proclaimed that "Jim from IT" was gay to save her from future heartache, or how he had apologized so kindly during the Christmas party.
Yes, Sherlock Holmes was an idiot, but she cared for him, just as she knew he cared for her.
It hurt Molly tremendously to see him so depressed. He did not bustle about her flat or fill up the space as he was wont to do. He ran no experiments, asked for no bits and pieces from the morgue, did nothing that she expected. Most shocking of all: he actually ate and slept when she told him to. In reality, he probably didn't even taste the food he ate, and he was probably lucky if he slept, but he didn't argue the way he always had. He hardly spoke at all, beyond a polite goodbye every morning and a civil greeting every evening.
He was so...empty.
This man was a shell of Sherlock, eating normally and recovering from a broken collarbone before he could set off with his mission. She had seen the fake documents that his brother had given him before, the unfamiliar and strange name on them. Linus Sigerson. In time, when Sherlock's injury was healed enough, he would bleach and shear off those lovely curls of his, use the food Molly got him to eat as a subtle padding, take to wearing slightly oversized clothes of mediocre quality and fairly poor taste.
Oh, yes, Molly knew precisely who Sherlock would become, and she hated Linus Sigerson with every inch of her being. Sherlock was tearing himself apart in order to build the disguise. She was only grateful that it would keep him safe. Well, safeish.
And when Linus Sigerson had eradicated every last fly in the web, when he had cleared his original name, when he could be absolutely certain of everyone's safety (including her own, touchingly enough), he would come back as the Great Sherlock Holmes.
She only hoped it would be soon.