Here's my take on what happened between the "I love you" scene and the final montage in TFP. I realize this has probably been done to death, but here's my take on it anyway. I realize the quote I used for the title isn't actually the quote from the show, but it sounded better for how I wanted to use it. Enjoy!
When she hears the sharp knock, Molly sighs and leans back into her sofa cushions. She considers ignoring it, but she has been expecting him to show up for hours, so she reluctantly pushes herself to her feet and strides to the door.
She yanks it open (perhaps with a little more force than absolutely necessary, but she's entitled after the day she's had), ready to verbally rip him to shreds for everything she has gone through on his account.
It is not, however, the Holmes brother she is expecting.
"Mycroft! What are you…. Are you alright?" she asks as her eyes take in his appearance. His normally impeccable suit is rumpled and soiled, and his expression is the weariest and most vulnerable she has ever seen.
"Doctor Hooper," he says, nodding his head in acknowledgement. "May I come in?" He ignores her concern, which tells her more about his state of mind than he probably realizes. Or wants.
"O-of, course." She moves aside, curious to uncover the reason for his visit. He usually calls when he wants to meet up. This is only the second time he has shown up on her doorstep unannounced.
She doesn't like to think about the first.
(Visions of an injured and depressed consulting detective flit through her mind before she brushes them away. Now is not the time to remember the day she helped Mycroft Holmes kill his brother.)
She gestures towards her sitting room, making sure he is seated comfortably before moving to the kitchen. "I'm afraid I'm all out of biscuits, but I could make some tea if you'd like?" she calls to him, taking out her kettle when he answers affirmatively.
She calms her nerves as the water heats up, pondering Mycroft's disheveled appearance. She wonders if it is connected to the mysterious call she received from Sherlock yesterday, but cannot fathom why Mycroft is here instead of Sherlock.
Then again, maybe his visit involves a completely different matter, and the two occurrences are not related at all.
(She's been around the Holmes brothers too long to truly believe that.)
When the tea is ready, she pours two cups and fixes his with cream and sugar, just the way he likes. She hands him his tea and sits down across from him, gazing at him over the rim of her cup.
(During the two years after The Fall, she and Mycroft had developed, if not exactly a friendship, then at least an acquaintanceship of sorts. Molly suspected that he sought her out because he needed to be around someone else who knew of his brother's not-quite-so-dead status. It was a feeling she understood well.)
They sip their tea in silence for several minutes, until Mycroft sighs and sets his cup aside. Molly looks over at him, giving him her full attention. Whatever he has come to say is obviously important, judging by the tense manner in which he holds himself.
"Doctor Hooper," he begins, but Molly cuts him off.
"We've been over this, Mycroft. Call me Molly."
"Molly, then," he says slowly. He blinks several times before continuing. "We need to talk about Sherlock."
Molly laughs bitterly, the pain from yesterday not having abated at all. She stares down at her hands, gripping her tea so tightly she is amazed the cup remains intact.
"I hardly imagined you'd just popped 'round for a chat," she quips half-heartedly. She pauses, her expression turning serious. "I suspected Sherlock was involved somehow."
"He always is, is he not?" he responded quietly. One corner of her mouth tilts up in commiseration. She knows as well as anyone how easily one's world can become centered around Sherlock Holmes. It is one of the reasons she and the man before her have retained their relationship, even after Sherlock returned from the dead.
Mycroft does not speak for several minutes, and Molly grows antsy with anticipation. "Why are you here, Mycroft?" she asks kindly, taking another sip of her tea. The warm liquid soothes as it slides down her throat, a comforting shield against the chill in the room.
"I owe you an explanation. When Sherlock called you…" He trails off when Molly raises a hand. She's sure he can see the pain on her face, the memory a gaping wound that hasn't been allowed to heal yet.
"Why isn't Sherlock explaining himself? Sent you to do his dirty work, did he?" It hurts, the idea that Sherlock would not even come to offer his apology in person.
(If she ever needed proof that she is just a means to an end, here it is.)
Funny, when he'd said he loved her over the phone, she had almost believed him for a moment. The first "I love you" was hesitant and strained, but the second….
"Sherlock does not know I am here," he says, interrupting her train of thought. "He would be rather… upset, if he were to think I am meddling in his life again."
"Meddling?"
"As I am sure you have noticed, my brother is not the most… forthright, when acknowledging his emotions. I am, regretfully, largely to blame for that." He swallows, and Molly realizes that this is the most open and honest he has ever been with her. She quite likes this side of him.
"The other reason is he is so closed off…."
Molly moves closer, sitting next to him and covering his hand with one of hers. She squeezes it lightly, urging him to resume.
Finally, the dam breaks, and words rush out in rapid succession, so quickly that Molly finds it difficult to keep up. He tells her about a third Holmes sibling. She can barely contain her grimace that there's another one, but she succeeds, somehow. She cannot, however, stop the gasp that escapes when he reveals the plot that Eurus had devised for her brothers.
(She's even more shocked when she learns of her ex-boyfriend's involvement.)
He lowers his voice as he describes a room with an empty coffin, the words 'I love you' etched onto the lid. Molly releases his hand as pieces start to fit together in her mind.
Sherlock had told her it was important that she say the words. That it was for a case. She had understood, deep down, that he would not ask her to say that without a good reason, and now the desperation she'd heard in his voice makes perfect sense.
"I have… never seen him lose control like that," Mycroft reveals. "He was nearly out of his mind at the thought of hurting you."
Molly cannot stop the small smile that appears on her face. "Really?"
A solemn nod is the only reply she receives.
After he finishes relating their encounter with his estranged sister, including John nearly drowning in a forgotten well, he reaches inside his coat and pulls out a flash drive. He places it in her outstretched palm, standing once her fingers curl around the small object.
"Will you do me a favor, Doctor-, Molly," he corrects. She smiles and nods. "Will you watch that for me, please? If anyone deserves to see it, I believe it is you. It might give you a little more insight into my brother's… feelings… when it comes to you."
She clutches the drive tighter between her fingers, knowing that whatever is on it will probably alter her relationship with Sherlock Holmes forever.
(The little sapling of hope she has been trying to stifle since Sherlock's phone call blossoms anew.)
He moves to the door, but abruptly stops and turns around. "Might I also request that you allow some of my colleagues to examine your home? I would like to ensure that my sister did not leave any surprises for you."
She glances nervously around the room, eyes darting between every dark corner as though James Moriarty could jump out at any moment. She gulps. "Of course."
He bows his head and turns once more, hand on the door handle, but stills when Molly's voice rings out.
"I thought you considered caring a disadvantage."
He tilts his head and observes her silently for almost a minute.
"I have had time to consider and amend my earlier assessment. I actually think you will be quite good for him, Molly Hooper."
She is still beaming when the door closes behind him.
This chapter was inspired by a lovely anon who left some Mycroft x Molly friendship head canons in my Tumblr inbox, as well as a post about Mycroft showing Molly the footage after everything was over. Part 2, detailing Sherlock and Molly's reunion, should be up in the next few days. I hope you liked it, and would be thrilled if you would please leave a review!