A/N: Spoilers for S3E01 "The Empty Hearse"
"My dear Watson," said the well-remembered voice, "I owe you a thousand apologies. I had no idea that you would be so affected."- EMPT
Sure, he'd laughed at Sherlock's stupid snide remark about how killing him was "so two years ago," yeah, whatever. He was allowed to laugh; he'd almost just been blown to pieces. And his laughing didn't mean that he wasn't still well pissed at Sherlock, even after the bomb had been defused. The man had pretended to be dead for three years and then showed up while John was attempting to propose with a marker-drawn mustache. Yeah, still pissed
It wasn't until later, when he'd calmed down enough to think back about the two and half minutes on the train, that he realized what had happened, what Sherlock didn't want him to see, what Sherlock was covering up with his asinine little "joke": Sherlock had apologized. He had truly, genuinely apologized, croaking out a deep and hoarse and quiet "I'm sorry." He would have known that there was an off switch the whole time—he'd called the police, hadn't he? He was acting when he was pulling the prank, but the apology was real. Sherlock had contrived the whole situation just so that he could give John a heartfelt apology, but, in typical Sherlock fashion, he didn't want John to recognize what was happening. He didn't think John would notice.
But now, John was the one with the upper hand. He'd heard the quiver in Sherlock's voice, and this time, John was going to be the one who knew something that Sherlock didn't.