A/N: This is brought on by a profuse amount of Goo Goo Dolls and alcohol, so forgive me. I also haven't seen Season 2 more than once, so I'm only going by memory. Also, because it's customary, I don't own any of the characters. Like you couldn't tell.
Molly watched Sherlock work. She was fascinated. From every delicate drop of acid into the main solution to the calculated, careful way he adjusted the microscope to just the right distance, she watched. She wished he would be as carefully calculated with her. She had practically thrown herself at him. She had applied lipstick and offered him coffee (and, if he'd paid attention, herself) in the middle of working in a morgue full of dead bodies for crying out loud. All of that in order to watch him break down the post-mortem bruising of corpses. What a waste.
She just couldn't get over him. His pale skin, tall figure, and his cheekbones that he seemingly purposefully set off with his coat lapels, all intrigued her. She dreamed of him at night; his piercing glance going over every inch of her body, much to her enjoyment, deducing the cause of every scar, observing every freckle. She imagined him slowly breaking her apart like a complicated chemistry problem, like she was no more than simple biology, muscles connected by ligaments and frail tissue. It was erotic really. This X-Ray image of her she thought Sherlock would have in his mind.
Even when he shot down her happiness in dating Jim, she could forgive him. After his string of deductions, it was impossible that she hadn't noticed the obvious signs. Of course Jim was gay. The only question remained: why hadn't she seen it before? Everything Sherlock said was right. And Jim hadn't even tried to sleep with her. She should've known long before. Why was she so stupid? She broke it off that evening after their date. Jim was understandably upset and when he had blamed Sherlock's "slip" of a comment about being gay, Molly couldn't control herself enough to lie and Jim took that as enough proof. She never saw him again. He had transferred jobs and any whisper of him being a murderous psychopath at the center of a web of crime never reached her. Sherlock didn't have the heart.
Aside from that moment, Sherlock had never interfered in her life. He had come and gone, quick as the changing breeze, intent upon one experiment or another. Molly didn't mind his presence. She only hoped he would mind hers. She clung to the desperate hope that he would look her way with interest, would whisper in her ear, would wake up with her some morning after a wild night. She eventually resigned herself to the idea that he would never do any of that. That he would forsake her for "the game." That she meant nothing to her.
Then one day he came into the lab, eyes wide, seeing beyond the lab equipment.
"Molly, I need you. I've always needed you." He gasped, practically beyond his tether.
Her heart jumped within her. He needed her. Oh God, it was the day she'd longed for, dreamed for even. And then he explained. She was brought down to earth with the practicality of it all. She was to assist him in a fake suicide. It wasn't romantic; it wasn't every girl's dream. It was simple, straightforward really. She was to help him escape the murderous clutches of an unnamed enemy.
And then Sherlock jumped…and he died to the rest of the world. Only Molly was left with the secret, with the pain, with the lie. She was left to watch John slowly dissolve into his limp again. To watch Lestrade flounder at case after case with the bodies in her morgue. To watch the occasional anomaly pass under her fingers uninvestigated, undiscovered. She couldn't say anything. She was sworn to secrecy that only love and dependency could bind so strong.