This is my take on what happened at the end of "Going Home" and some small theories on what happened before Killian got to our world.
He stares at the closed door. He can hear her behind it, he smiles at the thought that she is really there. He has imagined and dreamt of this moment for a year now, his swan always in his mind, living up to his promise that he would never forget her. Still in pain, Killian limps down the hall and to the elevator. He knows she will need some space to get over the shock but he knows that he will need to persist if he is to restore her memories. Limping out of the building and to the room he has rented, he thinks over the plan on how to restore Emma's memories. It was discussed between Emma's parents, Regina, Neil and the rest of the group the best way to restore her memories. They all knew her well, and knew that doing it wasn't going to be an easy job for Killian so they all came up with different strategies and left of for him to decide as no one knew what Emma's life would be like, a year on.
He thought over those few moments, seeing Emma in her pyjamas, he thought she looked so beautiful. It had been a whole year and all he wanted to do was touch her, to feel that she was really there, that he wasn't just dreaming again. He smiled at the memory of her pushing him away, that's my Emma. He knew she would fight him, she's a tough lass. Killian had a way for Emma, Henry and himself to get home, the potion and some fairy dust so he wasn't worried about that. Restoring Emma's memories would be the challenge. He decided that he would use a little of everyone's plans to get Emma to remember. She needed to know that her WHOLE family was waiting for her, that she was loved by so many.
Killian laid back on his bed and planned where he would start. The boy's father would be best to start. He needed to remind her that Neil wasn't just the man who abandoned her, but of the connections he had to the people waiting for her in the other world. Right, that's where I'll start, I just need to convince her to come with me. Maybe if I can just talk to the lad, he might be able to help. He didn't know what to tell Henry. Regina had said that he would have lost his memories too but having the heart of the truest believer; she didn't know what he could and couldn't remember. They had searched the area where they had arrived for Henry's storybook but it couldn't be found. They all hoped that somehow it had reached Henry and that he believed in them.
Killian thought of all the other plans that had been given to him. He knew that after working on reminding her about Neil that he needed to work on convincing her that he had parents who loved her. Knowing the Emma would still have the memories of growing up without her proper family, this would be difficult. He knew how much trouble her family was in and he needed her to understand that they were real and needed her help.
As the sun slowly dipped below the towering buildings in the city, casting his room in an orange and red glow, Killian's thoughts drifted back to Emma and their time spent together. He remembered a particular moment in Neverland when he had told her that he had yet to see her fail. Killian knew that somewhere in her mind, she remembered everything. Well he hoped anyway. And isn't that what this whole mission was about? Hope.