Disclaimer: I own nothing of Sherlock BBC and/or Doctor Who.
Molly Hooper considered today to be an ordinary day until a man entered the morgue. "How are you doing, Molly? Fancy a trip across time and space, the adventure of your lifetime? I'd asked you once before but you declined so I'm asking you one more time just to be super sure." The Doctor titled his head and waggled an eyebrow at her, perfectly portraying the image of a child going trick-or-treating during Halloween but the pathologist knew better.
"My shift is over anyway. Let's go, Doctor. Anywhere you want." The Doctor came up with a bitter grin at Molly's last sentence. That was the crux of it all, wasn't it? The mighty Time Lord could go anywhere he desired, anywhere but the bloody fixed points in time including the one that Amy and Rory resided in. The pathologist quietly slipped her hand into his and squeezed gently. The Doctor looked down and patted Molly's hand as the pair walked into the Tardis.
"We fought with a group of alien refugees that had huge fangs," The Doctor bared his teeth to illustrate the point, "and stopped Venice from becoming the second Atlantis." The pathologist squinted at him, "So Atlantis was real?" He nodded eagerly, "Oh yes, Molly, it's real, very real and technically, they were aliens too but much, much friendlier than those we encountered in 1580."
The Doctor then brought Molly to 19th century France where "We met Vincent Van Gogh and Amy tried her best to rescue him but his fate remained unchanged…Well, we reached the daily limit of sad tales, didn't we?", post WW2 London to "Say hello to my dear old friend, Winston Churchill", and lastly the Central Park in 21st century New York City.
The Doctor and the pathologist stood in front of a tombstone and neither spoke for a long period of time. The wind blew on softly, as if it were Amy and Rory comforting the Doctor and telling him that it was alright except it wasn't. Everything was not fine because they were dead, because he was unable to save them.
Molly broke the silence, "I do not know her as well as you do, Doctor but I would hazard a guess that if she knew the ending of her story right from the start, she would still go with you. You can mourn for their passing and you were when you brought me to the places that you went with them in the past but you should also celebrate the time that you had spent together. I always believe that if I truly remember someone, they will forever live in my heart and as far as I am concerned, they never left."
"I assume, like the first time, you are not going to stay around?" Their eyes connected and both of them knew very well her answer to his question. "He still needs me; at least that's what I think and so long he needs me, I will be there for him. You can always come and visit me, Doctor, whenever and wherever." The man in a bowtie kissed Molly's forehead and said, "Sherlock Holmes is a very lucky man and for your sake, I hope he realises that."
The way I see it, every life is a pile of good things and bad things.
The good things don't always soften the bad things, but vice versa, the bad things don't necessarily spoil the good things and make them unimportant.
Author's note: If I made any mistakes in regards to the designated universe, do forgive me (research could only get me so far).