AN: While they're not linked strongly enough for this to be considered a second chapter or part of the same series, this takes place after 'Highs and Hellos'. Reading that might give you some insight into why Mycroft feels the need to keep checking up on them, but certainly isn't necessary!
Mycroft Holmes had his own key to 221B Baker Street. Mrs Hudson had given him it freely when Sherlock was still using and lived alone, so that he could check up on him. While he hadn't had the need to do so for the drugs since John's arrival in his brother's life, he still worried enough to grant himself entry when they were both home but were not answering his calls. Sherlock made a habit of not picking up (though he normally shot off a text if pestered enough) but John was normally good at keeping the communication line open.
On the first instance of Mycroft's sudden and uninvited appearance, Sherlock had John bodily pinned beneath him on the floor. Both of them were panting and in a state of disarray – hair no longer neatly styled, clothes ruffled. Mycroft simply stood and stared in what he hoped appeared to be an apathetic manner. Both flatmates turned to regard him. John glanced quickly back at their position, apparently realising the connotations, and groaned.
"Not what it looks like," he pushed at Sherlock to get him to move, but all he did was lazily sit up.
"Physical combat training," Sherlock stated, clearly annoyed at the interruption (or possibly just at seeing Mycroft). "Yesterday's case proved that we are both out of practice. Unless you feel like joining in – and I would happilypractice my offensive techniques on you…"
"I'm quite alright, thank you," Mycroft's smile was tight-lipped, his grip on the handle of one of his ever-present umbrellas tight. "I'll leave you boys to it. No actual grievous injuries, if you please,"
"Oh, just get out," Sherlock sneered, before yelping as John effectively flipped him and caught him in a headlock. "John, that was underhanded!"
"Do you really think any of us will care when it comes to getting the serial murderer locked up?" John asked, proud of himself. While he had been trained in his time with the army, Sherlock had seemingly spent most of his life becoming an expert in the martial arts (Bartitsu, to be specific, Sherlock informed him after besting him four times in a row). Sherlock chuckled, not seeming too offended. Mycroft sighed and turned to leave.
On the second instance, John was straddling Sherlock's thighs on his brother's favourite armchair. Sherlock had both hands on John's waist, John had both hands on Sherlock's face, and their noses were almost touching.
"Good evening, brother," Sherlock said irritably, not moving. Mycroft had paused with one hand on the door, ready to escape should he really not want to see what they had been doing to end up in such a position. The muscles in Sherlock's neck twitched as he tried to move his head to look at his brother properly, but John's firm hands jerked it back into place almost immediately. The noise Sherlock made conveyed his mood perfectly.
"Your idiot of a brother managed to throw a cocktail of chemicals into his own face," John informed him in a tone very similar to that used by their nanny whenever Sherlock's habit of disobeying her orders got him injured. "I'm trying to make sure he won't go blind – oh stay still, will you? I'll give you a lollipop if you're a good boy,"
"I keep telling you, they weren't corrosive or otherwise harmful, anything would sting if it got in my eyes and you washed it all out anyway- damn it, Mycroft, don't just stand there and gawp, help me!" Sherlock snapped, pushing at John. His patience had apparently disappeared in a puff of smoke.
"I think the good doctor has everything in hand," Mycroft smirked. He hoped this would be a lesson Sherlock would learn from. Ignoring his brother's protests, he called a quick goodbye and left.
On the third instance, Mycroft was significantly more shocked. Two sets of men's clothes were strewn haphazardly about the room, their owners lying pressed together and covered in blankets. John was bright red and groaning, Sherlock snugly tucked against his back. The only other details Mycroft could gather were that Sherlock was probably still wearing his underwear – he could only see one pair of boxers, curiously wet and not in his brother's size – and that his hands were somewhere near John's waist.
"Honestly Mycroft, get your head out of the gutter. He's hypothermic, fell into the Thames," Sherlock said, frowning, his voice quiet for fear of hurting John.
"You p-p-pushed me in!" John protested, his frozen mouth clearly not yet up to plosives but sounding surprisingly strong for somebody who was potentially seriously ill.
"Away from the man who was going to stab you in the groin. Be thankful," only Sherlock would expect somebody to thank him after pushing them into a filthy river in the middle of London's biggest cold snap in years.
"Anything I can do? Phone an ambulance, perhaps?" Mycroft asked, feeling some concern for his brother's flatmate-and-possibly-more. At the very least he felt he needed to compensate John for his trouble.
"He doesn't need one, this exchange of bodily heat will suffice. Make him a drink, would you? Something warm, non-caffeinated. I'm already occupied, as you can see,"
Mycroft nodded tersely, doing as he was asked. And that is how the covert ruler of Britain came to be making hot chocolate for a humble ex-army doctor (who happened to be naked in his brother's arms).
The fourth instance was harder to write off as anything but what it was, as much as Mycroft wished otherwise. John had Sherlock pressed up against a wall intimately, his forehead on the detective's shoulder. Sherlock had one foot on the floor, the other leg wrapped around John's waist, his arms similarly employed half for balance and half for clinging on. Both pairs of trousers, underwear and shoes had mysteriously vanished, leaving them bare from the waist down other than their socks.
John either hadn't noticed Mycroft's entry or didn't care about having an audience. Sherlock, however, called his brothers name sharply and breathlessly in warning. John froze, his head recoiling with wide eyes to stare at his lover. It was a good job he didn't lose his footing.
"Excuse me?" he asked, clearly somewhat disturbed, shocked and offended. Sherlock growled.
"I suggest you leave now and don't use that key again," Sherlock didn't appear embarrassed in the slightest, hazily meeting Mycroft's stunned gaze. Then again, he was so flushed to begin with that any blush would go unnoticed.
"Buggering hell," John groaned, his head falling back down to its previous perch. He, on the other hand, was definitely embarrassed.
Judging it best not to speak, Mycroft nodded, pivoted and shut the door behind him. His key was discarded in a place Sherlock would know to look for it later.
After all, he had no desire to walk in on them again, trusted John with Sherlock's care, and could always get another key cut should circumstances call for it.