The first day they knew each other, John didn't know if Sherlock would live to see the second. It was sheer instinct that drove him grab his gun prior to leaving the flat, but that instinct had saved Sherlock's life. Both of their lives, he realized years later.
And so began the crazy life of John and Sherlock. Sherlock and John. And all the while, John worried about how it would end. First Chinese smugglers, then syntex vests and pools of fire and chlorine. There was leaping over rooftops, in front of cars, before the inevitable finally caught up with them. Not in a hail of bullets or a fiery bomb, but in a teary confession and a small step from a tall building. John never believed that Sherlock was the only one to die that day, as he watched his life and his friend fall, helpless to do anything to stop it.
John got his "one last miracle" and many, many more after that. He still worried for the end, but now it was asphyxiation from an experiment gone awry or anaphylaxis due to the bees. In between, there were still the cases, the puzzles, tea and toast in the morning, takeaway and Cluedo at night (though they swore every time was the last time). There were kisses and tears, making love until sunrise then sleeping past noon. Bees, cabs, jam, and guns, all such small things, but all vitally important to the story of them. Above all there was love; a love few understood but all envied, because who doesn't want someone to look at them the way Sherlock looks at John, John looks at Sherlock.
In the end, it wasn't bullets, bombs, psychopaths, or bees, but old age, one of lung cancer, the other of heartbreak, two hours apart, "I love you" on their lips and the other in their arms until the very last breath.