We know John hasn’t actually forgiven Mary. Either:
John’s being honorable and going back to Mary for the baby
John read the flash drive, lied about it, and is plotting either by himself or with Mycroft (not Sherlock)
There are some weird looks that imply he read the flash drive:
1) When Mary asks if John read the flash drive, he deflects twice and doesn’t answer:
MARY: So, have you read it? JOHN: W-would you come here a moment? MARY: No. Tell me. Have you? JOHN: Just … come here.
Deflection, a classic lying tell. And a very “John” lying tell; he’s not good at straight-up lying, so he doesn’t lie. He doesn’t answer the question at all. When else does he deflect? When he says “I’m not gay” in answer to questions about his feelings for Sherlock.
2) John looks down and turns the flash drive over in his hand, looking at it, when Mary asks him about it:
He’s definitely thinking something over. I don’t think that he’s wondering if maybe he should’ve read the flash drive after all – thinking “This is my last chance to back out” – because that’s not really in John’s character, and he has had six months to decide. So this is another lying tell from John.
