But what if? What if we knew what exactly was going on in those moments in between director's cuts? I took a shot at it.
-MISSING MOMENTS FROM THE FINALE-

She was so unconscious of what surrounded her, she seemed so out of her depths in the enchanted forest of 30 years ago, and Killian found himself biting back words of concern ad he tried so hard to look after her without letting her know. She'd have jumped right in the lion's den, (a.k.a. she'd have risked pissing off the Evil Queen) if he wouldn't have pulled her back. She looked so beautiful and more unguarded now in that outfit and attitude, the way she smiled knowingly at his appreciative glances left him a bit baffled, they were in great danger and she never let him get off that easily for flirting with her before. Somehow something looked different in her now, she didn't just pull away when he drew her hood up and they held their eye contact, and Killian didn't really know what to think. They were walking on the street now, close enough to touch but the closest they actually got was just as much as their clothes would brush, when they heard a carriage approach.
-

The Dark One was clearly the last person he'd like to meet in a trip to the past but desperate as the situation was he'd actually didn't feel the urge to kill him as he once would've. Hearing Emma spoil all the future got him a bit frustrated but at the same time it actually was kinda funny, thinking how everything turned out to be for the inhabitants of the Enchanted Forest in their future lives.

After leaving the castle he explained to Emma his plan and they went to the tavern. Gods was it weird to watch himself across the room. He tried to sit comfortable and pretend like he didn't think that that bloke over there was a bit too drunk and a bit too vengeful to be in the same room with his Swan but it was frustrating in a way, to be pissed with himself, and a lot weird as well. "Here I am, rather dashing, don't you think?"
"Is this even a good idea? What about preserving the future?"
"I'll be fine, giving what I'm drinking, if I'd remember anything I'll simply blame the rum. Just make sure that I.. him stays occupied and doesn't return to my ship and I'll take care of the rest" he said looking away pensive.
"Ok" said Emma behind his back and just some seconds after he heard the noise of her cloak falling down and when he turned to look he saw her loosening her corset and he heard his heart skip a bit as he said in high pinched voice: "Wait what are you doing?"
"Making sure he stays occupied! Shouldn't be difficult" she said before leaning in and finishing the sentence "You and I both know, I'm his type"

Gods this woman

They both jumped up and he closed the gap between them saying "Swan, that man sitting there, You don't know him... just be careful"
"If I didn't know any better I'd say you're jealous" at that Killian felt his cheeks flush and unable to reply he simply staggered out of the tavern

Emma was walking back to the ship with Captain Hook of the past, whom she'd gotten really much drunk, and still he was sipping that bottle of rum like a dying man. She looked at the wavey way he walked by and somehow she hoped he'd pass out so that she could stop herself from making any more messes. When Killian warned her she had to laugh a bit, he thought she was used to princes and noblemen, but apparently Killian didn't still know that much about her world without magic and the male population in it. Drinking with past- Hook had been terribly funny and very flirty, but even deep in the drunken state and given the pirate status, still the man was really gentleman-ish in a way and it surprised Emma. Of course she knew the extent to which he planned to go, but after all she approached him to get him to pretty much react like this so she couldn't blame the bluntness, she had only just met him in this world. She thought again of her present Killian and the way he looked worried about his past self and she smiled to herself again. She had many worse dates than this, granted, and with less dashing subjects too. When she spotted Snow she pulled him back to hide away and said "Woah I think I should rest for a moment" and before she could really do much about what was going to happen next, Hook grabbed her and held her up in his arms leaving her baffled and a little out of breath "No, no need I've carried rum barrels heavier than you" and with that Emma spotted Snow snuggle away and relieved said "Actually I feel much better", but he kept her up close to his chest and moved forward still before yelling "Behold! The Rolly Jojer!"
It took all her restraint not to laugh.

He punched him. Wait no, he PUNCHED HIMSELF!
"Are you kidding me? How's that not gonna have consequences?"
"He was asking for it, and like I said he blamed the rum, now let's get out of here" he gestured toward the stairs hastily. She obliged stunned and honestly a bit weirded out. The man now behind her honestly didn't want her to be with the past him. Which meant he regretted being like that to some extent. Walking off the plank and on the docks again she realized how much this man had wanted to change for her and she couldn't help reaching out for him, grabbing his good arm, and leaning in while saying "Poor Killian, that pirate has really gotten on your nerves" she said in a light tone, then when he turned his face to hers she added "don't worry he wasn't all that bad as you think, he was kinda nice, I'd say he's got some potential" she smiled at him trying to let him see the joke in her eyes, and she relaxed when he tensed down a bit and once again he put up that little school- boy kinda of face and he looked away with a bit of rosey cheeks. She couldn't help it and she went in for a little kiss on his cheek and then she said "Don't worry I think I prefer this version of you, although I have to admit, I liked the red vest better" and with that she let go of his arm and walked past him grinning to herself.

And here he was again. This little town in the middle of a completely foreign land. Everyone and everything looked exactly the same as before, and after he'd seen the mystery woman in the diner he collapsed on a chair just outside the little royal's party. He needed a sip or two of his rum. He's probably been living in a dream or something. After all he and Emma have been through already going back in a time and place where he was solely concerned on getting revenge for his lost love and thought he didn't have another shot at happiness left him dealing with mixed feelings. He didn't miss those days, and to some extent even his life as a pirate didn't really looked so great from this new point of observation.
Once again it felt obvious how all his wandering and waiting around for revenge was written in the stars, otherwise he never would've found Emma, his Swan. No matter what he went through to get to her both unconsciously and not he didn't regret anything now, if he just thought of how vulnerable and beautiful his princess had looked just about yesterday and how grateful he was that he had gotten the chance to be there for her to help her and comfort her.
He kept seeing her swinging to the rhythm of the waltz just there, in his arms and his heart felt warm. He took another sip of rum –nope, still unbelievable- he though.
He didn't see her approach him, and quite frankly he lost the notion of time, so he was surprised that she specifically came outside to check in on him. Or at least he thought that this is what she wanted to do.
"So, Do you think Rumplestilskin's right? I'm in the book now" se said, and he had to silently chuckle "He said everything besides our little adventure would go back to normal.. do you think that it is?"
"He's right" he replied, then he thought he would drop a little flirty remark to test the waters "otherwise I'd remember that damned bar wench I kissed"
Emma smiled knowingly "How would that prove anything?" they were both exchanging smiles and repressed laughs now when he replied in all seriousness "I know how you kiss. I'd have gone after her, but I didn't, my life went on exactly the same way as before"
Emma smiled, looking pleased but at the same time kinda unsurprised at his response as if he only expressed himself in this flirty way... which he didn't. Did he? "Yeah, must have been the rum" she said.
"Everything's back to normal. You're a bloody hero Swan" he said as he stared at her . Her spontaneous smile reached her eyes when she said "So are you" and here he was chuckling again – gods was it weird to be called that- while he bowed his head "I wanted to thank you Killian," his attention back to her face, he heard her say the words he waited to hear for quite some time "..for coming back for me in the first place in New York. If you hadn't..." those words he had been missing were now finally filling a void. He had done something good for her and she's seen the truth and his good intentions, so he got a small victory there. Good things come to those who wait apparently. "It was the right thing to do" he said tilting his head the side.
Emma seemed almost afraid to respond to that, but went on anyway "How did you do it? How did you get to me?" she finally asked. He heard himself take a deep breath: this was another moment he had been waiting for, but he only would have said anything if she asked. That little piece of the wall was still up between them. Of course he knows he's hid other things, but this bit of misinformation is somehow vital to.. whatever he and Emma have. The time had come. "Well the curse was coming, I took some of my crew and took the Jolly Roger as fast and as far as I possibly could to outrun it" she looked surprised and with a somewhat impressed and untrusty voice said "You outrun a curse" he smiled and said "I'm a hell of a captain –she was chuckling but he went on- And once I was outside the curse's purview I knew that the walls were down. Transport between the world was possible again, all I needed was a magic bean!" he finished simply- although it didn't sound or actually had been in any way simple.
"Those are not easy to come by" she said, amazed
"They are if you got something of value to trade" he said bowing his head again and pronouncing the last couple of words biting back nostalgia.
Emma was smiling when she asked "And what was that?"
"Why the Jolly Roger of course!" There, the cards where laid on the table now. He looked her expression change. There was shock, sadness and tenderness. "You traded your ship for me?" she said somewhat incredulous.
Looking at her, at all she meant to him and to everyone in this town he thought, -Yes, I did. I wouldn't have done it for anyone else and I'd do it again if it would get me back to you- but instead he only said
"Aye"

Split second. Emma was kissing him. Gods he loved it when she did. He felt happiness surge into him as he raised his hand to cradle her hair and he felt hers into his own, pulling him closer to her, and in a way he could've died in this moment if it wasn't that he felt so extremely alive right there. Emma's kisses always did the dirty work of somehow explaining her feelings without words coming out of her mouth. He couldn't really say he didn't like her way of expressing her deepest thoughs, expecially now that she turned her head and deepened the kiss. This kiss almost said "I'm sorry", "thank you" and "I love you" all at the same time.
It went on like that for a while, unlike Neverland he got to a round two and eventually three and four, coming out for breathing and smiling at each other, but keen on keeping it going, like never before.
Eventually Emma rested her forehead to his and, and breathlessly they looked at each other, smitten and smiling.
"Now what?" he asked smiling and lightly to her. To his surprise she didn't avoid the question but said "I don't know.. I'm not good at this, you are! I always do or say something wrong but believe me I care about you.. a lot. And sometimes what you say or do scare me off but.. I'm getting used to it, thanks to you" she was blushing so much right now it was 100% adorable "Look Killian what you did, I.. I know what that ship meant to you, and I'm sorry you had to lose her, it was all you had left of your brother and Milah and Bae so I'm really sorry about that. On the other hand I can't thank you enough for sacrificing it to bring me back home. I.. I think you know how I feel about you know, I'm just not yet ready for.. all of this but, please promise me you'll be here to help me through it and, please please please don't fall through any portal or piss off any villain ok?"
"Don't worry Emma, I'm not going anywhere" he said before kissing her again.

It was like being teenagers again.
They snuck back inside the diner, where people looked oblivious of what they have been up to in this 20 minutes more or less. They were giggly and it felt wrong not to hold hands, because they haven't gotten that much into intimacy before, and it was a sweet pain being so close but couldn't touch each other. She spotted her parents looking at them and she decided she wasn't up to be busted this fast so she urged him to turn his back and sit on a stall and then she ordered two cups of hot cocoa. The mysterious lady was just sitting there close to them and they were distracted by her questions on the future/present and they only had few time to themselves, between talks. They exchanged longing and knowing looks. It looked like none of them were about done of what they were doing before.
But then Regina entered the diner and things got complicated.
-

Killian was still amazed. Even with all this upcoming problems between Emma and Regina all he could think about was that kiss and the way Emma totally unconsciously put her hand on his shoulder that night. It was such a protective and at the same time possessive gesture that it talked by itself.
He was now waiting for her parents to leave to go to his chambers and have some rest. Henry left with a fuming and definitely heartbroken Regina, so he hoped that the young lad could soothe some of that pain out of his mother and calm her down, because otherwise that meant they were back on the initial page, only with Emma's life at stake this time.
After saying goodnight to her parents and walking back to the chamber in the corridor Emma's eyes searched for his and when they did his arms were almost already around her and she looked extremely tired but vulnerable and grateful for that and returned the hug.
"It's gonna be okay Emma, you did everything right, sometimes Regina doesn't see things clearly. She can't blame you for saving a life, that's just nonsense" She looked up to him with teary eyes and she tightened her grip on his waist and whispered "Thank you for saying this, I just.. I wish things haven't turned out like this. I had no idea of who she was so I can see her reasons in some way but, I know I did the right thing, my gut told me that.. It told me lots of things lately" she added, a shy smile creeping back on her face. He smiled back before leaning in and kissing her again, finally.
They went back in his room and they kissed a lot, but they wanted to enjoy this feeling as long as they could, not to go further that night. Killian, volunteering to be the gentleman for this occasion, suggested he could sleep on the floor, before Emma waved the idea off as silly and they ended up in his bed simply asleep under the covers and tangled in each other and it was the first good sleep both of them had experienced in a very, very long time.