Summary: John accepts a ride and Mycroft apologizes (as much as Mycroft is capable of such a thing).
A second missing scene from The Empty Hearse. Takes place directly after Mary leaves John at the clinic. Thanks to Jack63kids for inspiring me to finish this second bit. :)
Exterior of the clinic where John works. It's early evening. The car park in front is deserted. John exits the building and turns to lock the doors. As he turns back a large black car pulls up and stops directly in front of him. A man in a suit steps out of the front of the car and holds the back door open. John looks at the man, then the open car door and shakes his head. The man gestures at the open door and raises his eye brows. John doesn't move.
MYCROFT (we hear his voice only from inside the car): Please, John. Don't make this...difficult.
John takes a deep breath and gets into the car. The man in the suit closes the door behind him, climbs back into the front and the car glides out of the car park and into traffic.
Cut to the interior of the car. John and Mycroft sit on opposite sides of the spacious back seat.
JOHN: Can't say I've missed this.
MYCROFT: I always rather enjoyed our little chats.
John snorts, but doesn't reply.
MYCROFT: It was my idea, you know.
John looks up and meets Mycroft's eyes, keeping his face carefully neutral.
MYCROFT: I was concerned for the safety of everyone involved. You included.
JOHN (looks away, disbelieving): Concerned? For me? For...my safety?
MYCROFT: Well, yes. Of course. Jim Moriarty threatened to have you shot, or didn't you know?
JOHN (angrily): You think Jim Moriarty was the biggest threat to my safety?
MYCROFT (eyebrows raised): He was a psychopath with a death wish and team of assassins at his disposal. If you can think of a more dangerous person to have after you, please enlighten me.
John gives him a sideways look, one eyebrow raised.
MYCROFT (scoffs, rolls his eyes): You know what I mean!
JOHN (angrily): Don't insult me Mycroft. It wasn't ever about my safety. Neither of you thought I could keep your bloody secret. What I don't understand is how you could actually believe that I would ever put Sherlock in danger?
MYCROFT: That wasn't it, John. Please believe me. We needed your reaction to be genuine. There were people watching your every move. Dismantling Moriarty's network was an arduous task, especially for one man working mostly...
JOHN (angrily interrupts): For two years? Two bloody years!
Mycroft folds his hands into his lap, waiting.
JOHN (slowly, deliberately, pain clearly showing on his face): Do you know how many nights I sat in my flat with a bottle, and...and...my gun?
MYCROFT (after a long pause): He was held captive in Serbia, you know. He spent several weeks in a cell, being starved and tortured. They thought he was a government spy, which I suppose he was, in a manner of speaking. Very nearly got himself beaten to death at the end.
JOHN (swallows, anger dissipating at the thought of Sherlock being tortured): But he escaped, obviously.
MYCROFT: Not without considerable assistance.
Both men sit in silence for a long moment. John watches the city slide by as dusk falls outside the windows.
MYCROFT: I am sorry, John. Had I anticipated the amount of pain you endured, I might have...intervened sooner.
John gives him an incredulous look.
MYCROFT: Despite what you think, I've never enjoyed watching either of you suffer. And, you look after him in ways I never could.
JOHN (scoffs): He's been back less than forty eight hours and you're assuming it'll be just like old times. I don't think so. I've got someone else in my life now. Things are different.
MYCROFT: Yes.
JOHN looks momentarily confused, trying to figure out which statement Mycroft is agreeing with.
MYCROFT: You will forgive him, John.
JOHN: I don't know if I can. I don't know if I want to.
MYCROFT: It wasn't a question. Do you mind if I drop you off here?
John looks out and realizes they have just turned onto Baker Street.
JOHN: How did you... oh, never mind. Yes this fine.
The car slides to the curb just down from 221B and the man in the suit once again holds the door open.
MYCROFT: Good evening, John.
John climbs out and the car pulls away. He straightens his jacket and walks the short distance to the flat he used to call home, pausing outside the door. He doesn't notice the two men coming towards him until it's too late. They drug him and when he awakes, he's unable to move and his lungs are burning with petrol fumes and smoke. Thankfully, Sherlock and Mary arrive just in time to pull him to safety.