OH MY GOD I FIGURED IT OUT.
The episode isn’t disjointed at ALL! It all makes sense if you realize that JOHN IS THE CASE.
From the moment Sherlock confronts John in the restaurant and comes face to face with the full extent of his fuck-up, John is the problem he needs to solve, the thing he needs to fix.
Sherlock isn’t concerned about the terrorism case. He tells Mycroft he’s got it covered—and he has! Terrorism is hideous, but simple: the person’s motives are clear, their goal is clear, and Sherlock knows the who, when, and where. All he has to do is keep it from happening.
What HE is concerned about is winning back John. And he approaches that like a case. The whole episode is Sherlock investigating love and friendship. No wonder he reacts so incredulously when Mary casually says she’ll talk John around; she doesn’t even realize that what she’s saying in Sherlock-language is, “I’ll solve this before you can.”
He spends the whole episode performing research. He interviews witnesses’—Molly, Mycroft, Lestrade, his own parents, even freaking Anderson—to reconnect himself, remember what it feels like, how it works, how you navigate it, why it’s important. What it looks like to to the people who aren’t him.
He spends a day with Molly, with her filling John’s role. He tells her it’s a ‘thank you,’ and maybe it is. It’s also him spending a day with the only other person he knows who has a heart as big and loyal as John’s, a kind of shadowing/observation/inside look of the sort we so often see him do. It would also explain why he’s thinking about John so much in this scene.
He talks with Mycroft about loneliness, isolation and friendship. But this time, Mycroft is (unbeknownst to himself) playing the role of Sherlock, and Sherlock is playing the role of John. (He’s also trying to tell his brother, in an underhanded way, that Sherlock has discovered that friends are good and that Mycroft doesn’t need to be lonely, and also indulging in some brotherly gloating because Mycroft might be the smart one, but Sherlock has people who like him!)
He listens to his parents (who are, tellingly, dressed like Sherlock and John) talking about their relationship without even talking about it. They know each other so well, they complement each other so well, they’re so comfortable in their togetherness. How? How did they achieve this?
And at the end, his solution is, as Sherlock’s solutions always are, full of flashy, tricky cleverness. (Because it’s never enough for him to solve a puzzle; he always wants to be SEEN to solve the puzzle.)
And why, why why WHY, is Anderson’s scene the one that interrupts that fateful moment in the train carriage?
Anderson believes in Sherlock Holmes. Anderson is the one who never doubted him. Anderson set up a fake crime just so that Sherlock could have something to play with. Honestly I’m still not 100% sure what the scene with Anderson was supposed to accomplish (let alone whether it’s successful), but 1: in keeping with the episode, Sherlock is visiting every one of the people who, in whatever form, held faith with him while was gone, and 2: the scene definitely provides a contrast between Anderson’s confidence in the power of Sherlock’s intellect—he KNOWS he pulled it off and he’ll wait as long as he must to find out how—against John’s faith in Sherlock as a person.
Anderson breaks. ”No, that’s now how I wanted it to have happened.”
John doesn’t. He doesn’t care how (well, okay, so he’s a little curious), so long as Sherlock is there.
Maybe that’s another possible read on Sherlock’s bomb trick. He can’t fix it, though he’d go back in time and undo it if he could. All he can give John is that he’s here now. And John’s response is, Yes, I’m still angry, but it’s enough that you’re here now.
There are wounds that our loved ones can deliver us that can never be healed, that maybe we can never entirely forgive them for. But that doesn’t mean we don’t still love them.
I’m still in favor of their relationship as a kind of S&M game. But the point is, whatever kind of game Sherlock and John play with their lives (and there absolutely is one of some sort, whether it’s that or something else; there’s some set of rules by which they implicitly decide what’s okay and not okay between them), this was different. Reichenbach and the Hiatus weren’t playing by the rules, and they weren’t part of the game, and it wasn’t funny or sexy or cute.
And maybe Sherlock forgot that, because for him Moriarty WAS always a game. He and Mycroft always had a plan, always knew the rules, always knew there were options and that the risks were controlled. And he has always had a tendency to assume that John would know what Sherlock wants him to know via osmosis.
So it’s not that Sherlock ever forgot that John didn’t know he was dead. He just forgot that for John it was serious. (Because he’s a self-absorbed dick. But one who loves John.)