Sherlock is pregnant with John's baby and alone (maybe John is dead, maybe he's with Mary). Sherlock is depressed and has got a problem taking care of himself. Tired of seeing his brother this devastated, Mycroft decides to snap him out of it. I don't care what exactly he says, but what Sherlock hears is that if he won't stop being like this, Mycroft's going to take the baby away from him (maybe he and Greg can't have children of their own). Mycroft doesn't mean that, but maybe he sort of wants to threaten Sherlock into getting back to normal. Maybe he's worried that Sherlock's going to turn to a self-harming behaviour otherwise.

Sherlock, however, freaks the hell out and does whatever he can to cut all possible ties to his brother and Lestrade. He's scared and paranoid. He thinks that the two of them are just waiting for him to give birth so they can have the baby for themselves. With Mycroft's influence it wouldn't be a problem to take the baby away.

So Sherlock runs away and gets himself into a serious trouble. Maybe Lestrade and Mycroft have to save him, which only makes him think that they just want the baby to be safe and will dispose of Sherlock once it's born.

Of course, it's not true and they try to convince him that they wouldn't do anything like this. But even when the baby is born, Sherlock refuses to let either of them anywhere near his baby. Maybe he doesn't ever allow it.

The ending is up to you.

If John is alive, he can come back and fix everything, if you want.