People always underestimate John, despite John's toughness he has proved time and again and despite his military past (people don't become captains for nothing), so when another powerful villain appears, that person forgets about John, doesn't even take him into consideration, and goes for Mycroft and Sherlock. Idk, maybe the both of them get kidnapped, nearly killed, or are in grave danger in any other way when their situation is seemingly hopeless. The baddie nearly celebrates the victory when John appears and deals with them, saving Sherlock and Mycroft. If one or both are injured he can also switch to his doctor mode.

John/Sherlock would make me happy, especially non-sexual.