This chapter takes place during The Great Game. Thought I'd expand on the scene a little bit.
No match. No match. No match. The words kept flashing up on the computer screen, mocking him as his time to solve the mystery in front of him was ticking by. He wasn't bored anymore. No, whoever had sent him the phone, the shoes, was playing a game. The rules were scarce and the opponent, though he could guess, was still uncertain. John was pacing, worrying about the woman that was a literal ticking time bomb somewhere. Sherlock had learned early on in his detecting days that if he tried caring about the victim, it was a waste of time. Caring got you too wrapped up in the case and if you failed to save that person, you would fall hard.
Mycroft kept texting him, annoying him. Why wasn't he calling? It was much easier to just let him leave a long winded message. Why hadn't he cancelled his dental appointment? And where was Molly? He was coming close to a result and she loved hearing about his cases. Though, he would have to leave out the part about the woman being strapped to a bomb. John's empathy for others was annoying whereas Molly's was unsettling.
The computer alerted him to a positive result. At that same moment, as if it was planned, Molly came into the lab, smiling at him
"Any luck?" she asked, knowing the answer.
"Oh, yes!" Sherlock said. John moved away from the computer so that Molly could come and look at the results for herself. Sherlock was prepared to launch into his explanation of the soil samples before he moved on to deducing the shoes when the door to the lab opened and someone unknown to the consulting detective came poked their head inside. Molly was flustered upon seeing this man-she called him Jim. She was nervous, she was smiling, she was happy. Molly Hooper had actually found someone that lasted past one date. Maybe she might even have a long term relationship with him. Annoyed, Sherlock peered into the microscope again.
Molly had notoriously bad luck with men. Most of the time, they never called again once they heard what she did for a living. She'd go out on these dates for lunch, anxious and excited, then come back disappointed and she wouldn't be nearly as chatty as she normally was. For some reason, this one stuck past the first date. He was used to working with single Molly, working with in-a-relationship Molly was something he wouldn't look forward to; it gave him an uneasy feeling.
There had to be something wrong with this one. There was something wrong with all the others. There was the one who was cheating on his wife and his three other girlfriends, there was the one who secretly had a kid in America, there was the one that decided to propose marriage before dinner even arrived to their table, there was the one that said he was looking for someone he could settle down with but really just wanted to sleep with her and never call her again (Sherlock was lucky to uncover that one earlier than usual and warn Molly; he did not need an emotionally damaged pathologist), and finally the one that tried to flee the country after it was found he was involved in several online scams that cheated thousands of people out of their money. He always warned her when he found out these secrets and Molly would always be angry at these men and herself when Sherlock's deductions were accurate.
"Every time I think I find a nice guy, you come along and spoil everything," Molly said once, annoyed.
"For good reason," Sherlock reminded her. "Your emotions would affect your work and there is a serial murderer on the loose. How is that blood analysis coming along?"
Jim was trying to say something to him, annoying him. Molly was making bad jokes again. She liked this man, but there was always something wrong with them. She was always attracted to men that were bad for her and never to men that were good for her. She'd put on three pounds since he last saw her. Something had to be wrong if she was eating more sweets after work than usual. Sherlock looked at Jim, to see what was wrong with this one.
Oh! That was it! He found out what was wrong with this one, too.
"Gay," he said out loud before he could stop himself, looking back at the microscope. Molly was immediately alarmed, her smile dropping from her face. Sherlock tried to cover up what he said to Jim as the gay man clumsily left his number for Sherlock under a dish.
Once Jim had left the room Molly demanded an explanation from Sherlock, which he gladly gave her, even if he was 'spoiling everything' again. Jim was gay, using Molly as a cover for some reason. He was surprised Molly hadn't picked up on it sooner. However, he could tell her now, and his solid deduction would back him up. Rather than attempt any sort of long term relationship with this man, Molly should break it off now. Besides, they weren't exclusive, and clearly hadn't been out on that many dates. Sherlock was somewhat pleased with himself. This was his best timing yet out of all of Molly's attempts at romance. She would be happy that this had been brought to her attention sooner rather than later and Sherlock would have an unattached pathologist working with him again.
So why did she look angry as she stormed from the lab? Hadn't he done the right thing?
"Charming, well done," John said tersely. Sherlock turned away from the door, now that Molly was out of sight.
"Just…saving her time. Isn't that kinder?" He had been helping her out like this for the past two years. What was the problem?
"Kinder? No, no. Sherlock, that wasn't kind." Sherlock needed a distraction, he needed to get back on the case and not think about how he had ended another one of Molly's short-lived relationships, even if it was for her own good. Ah, the shoes. It'd be funny to see John try and make a deduction about them. He needed a laugh right about now.
If you watch this scene, Sherlock's expression when Molly storms out of the lab says a lot. It's like a "What? What did I say wrong?" type of expression. He was genuinely trying to help her out. I can see Sherlock interfering with a lot of Molly's relationships and pointing out what's wrong with them. Good in the long run for Molly, although I can imagine it's annoying.