Complete and utter AU (originally posted before 3B).
"This isn't an option, he'll understand, he has to." Emma thinks to herself. She grabs her jacket and car keys, heading down the apartment stairwell, "This is the only way."
She turned out the door, and walked briskly to her car, she quickly started it and drove across town the marina. As she got close she put the bug in park, got out and made her way to him. Killian rarely was anywhere besides his ship, unless with her at the apartment or Granny's.
She walked, with a mission, to his cabin below deck. "Killian," she called calmly, not even pausing to knock on his door, she walk into the room. The room they've shared over and over again. The room they got to really know each other completely. The room she'll might never see again. The reality of what she had to do fell upon her in the moment she laid her eyes on his back, he had been organizing the table in the center of the room. The sight of him brought tears to her eyes, she shouldn't have to do this.
He turned a few seconds after she opened the door, and saw the tears in her eyes, "Emma, Love, what's wrong?" he dropped whatever her had been holding, and made his way to her form in the doorway. "What happened?"
He wrapped his arms around her shoulders, pressing her into his chest, and her own arms went around his waist. "I have to leave," she told him, her voice muffled by his shirt. "It's the only way, I have to go and I can't take you with me."
"No, no Love, there has to be another way." he whispered in her ear. Emma shook her head, "There has to be another way," he insisted.
"Regina and Gold have checked every possible option, and unless I leave nothing will be okay. You guys will be fine, you can make it back safely. But I have to stay here, but I have to get as far from Storybrooke as possible in the next 24 hours for this to work. I have to leave now." she explained quickly. "I just want you to be safe."
"I need you with me, Love." he gripped her tighter, "I won't be comfortable knowing you're alone."
"Well, I won't be alone, exactly. Henry won't go without me. I need to keep him safe. And I still have my apartment in Boston, so once 24 hours are up we'll go there." She pulled away from him, wiping her eyes.
"I'll stay with you too." he declared, Emma immediately shook her head.
"They need you, you're the only one who can steer the ship with Neal already in the Enchanted Forest. And when they get everyone there they'll need you to help keep order and get everyone settled."
"They can't force me to go, they'll figure it out, please, Emma." Killian put his palm on her cheek, she shook her head again, but placed her hand on top of his, holding him to her.
"Please, go with them. You need to stay with my parents, make sure they're okay, please." she begged him. He gazed into her eyes and saw how much it pained her to ask this of him. Saw how much it meant to her.
"When I know they're safe I'll find you." he promises her. She smiles at him gratefully, tears sliding down her cheeks.
Emma pulls herself together, "I have to go, I have to get Henry." she moves away from him, and as she begins to turn away he pulls her back. Placing his lips on hers, he give her one last passionate kiss. As they open their eyes they say goodbye without a word and Emma walks away. Leaving Killian standing alone.
Four Years Later
It was an interesting thing, parenting. Emma never truly thought about everything it would take, how you had to be on your toes every minute. You had to sleep with one eye open, and you became this almost overprotective mom-ster, now she understood what Regina had meant, raising Henry.
The teenager was washing dishes in the kitchen at the moment, little Liam sat next to him in his highchair. Liam was almost three now, and Emma couldn't believe she made it this far.
She hadn't realize she was carrying a baby until it was over two months that her parents and Killian had been gone. She also didn't believe she'd be able to raise a child at this point in her life, but with her inability to let him go and with Henry urging her to keep and allow him to help her, Emma has made it .
When they made it to Boston and settled in she took up her bail bonds job again, and after realizing she was with child she began working mainly behind the scenes, on the computer. She was an important worker for them, so her boss had them keep up her expenses, so she could work and stay home to take care of her children.
Liam. Named after his father's brother, the story of his older brother was precious to him and she knew Killian would have wanted him to have that connection. Liam had dark hair and his father's bright blue eyes. He really resembled Killian so much, sometimes it hurt to look at him too long, Emma could feel his stare breaking her down.
"Liam, you want to dry the plate?" Henry asked, handing him his plastic blue plate from dinner.
"Yeah, rag please!" Liam replied. He was very smart, and so aware of his surrounding, he's been above average on most charts. The doctor said it was due her interacting with him daily and involving him in basic chore around the house. She got told by so many people she was a great mother, it was surprising to say the least.
Emma stood in the doorway to her bedroom, watching her kids from behind. She looked on for a few more moments, then turned back in. She was folding her clothing, hanging them, or place them in a drawer.
Minutes later there was a crash and Liam was calling for her, "Mama!" cried her little boy, "Mama!" he yelled at the top of his lungs, she could picture tears running down his face instantly, breaking into a sprint towards his voice.
"Oh, Liam, you're such a big baby, I told you not to do that." Henry said as she reached them, obviously Liam did something too big for Henry to overlook and upset him. And Henry being mad probably set off the two year old. She noticed, under the highchair, a puddle of water, along with a few large shards of glass. "He dropped the glass Mom, I told him not to grab it, but he did and it slipped onto the floor." the teenager explained.
"I see." she commented, Liam cries didn't subside, but grew louder. "Liam, sweetheart, you're fine Baby." she leaned over and put her face directly in front of his, holding his chin, then gave him a peck on the forehead. The brunette calmed and sniffled. "I'm going clean it up, okay?" Liam nodded in agreement and sat patiently in his chair.
She picked up the glass as quickly and carefully as possible, forbidding Henry to help, which he laughed about. She always took any chance she could to treat him like the ten year old she first met.
When she finished she picked Liam up out of his chair and told Henry they'd be in her room. "Are you going to help Mama fold the clothes?" she asked.
"Yeah!" Liam said bouncing on her side, she let out a laugh at his eagerness. Just as she was about to place him on her bed she heard a knock on the door. She peered at the clock, 8:45PM, someone was at her door at that time?
She went to sit him down again, she was probably imagining it. They never had visitors. As she placed him on the bed she heard another couple pounds on the door. "Mom, someone is at the door!" Henry yelled, then started running water. Well, he wasn't going to answer it.
Emma held Liam against her again and walked to the entrance of their apartment. "Who is it-" she asked opening the door slowly, the chain lock kept the space allowed narrow. She was cut off by the sight on the other side of the door. His hair, eyes, clothes; him. Killian.
She quickly undid the lock and pulled the door open, "Killian, you're here!" his arms were open and she ran directly into them, "You're back, you found us." she mumbled into his chest, her arms still wrapped around Liam, lost in her happiness.
Even though Killian was grateful to find her, the fact the she stepped into his embrace with a child was worrying. "Emma, of course I'd find you." he whispered into her hair, closing his eyes and cherishing her form in his arms. It had been so long, an eternity almost.
She pulled away, repositioning the child in her arms, then placing her left hand on his cheek, "I've missed you so much. Henry! Henry, Killian is here!" she called.
"Really?" a boy's voice called from farther inside the home. Suddenly from behind the wall an much older looking Henry appeared, "It's true!" he ran into the the older male, giving him a bear hug. "Does this mean we can go back with you now?" he asked pulling away.
"Aye, it does." he replied bring up his left hand to scratch his head.
"Woah, you have your hand back!" Henry realized, Emma noticed then as well, surprised.
"Yes, well, Rumplestiltskin thought to do something kind in return for all my help to him and the others. We thought this would be good." he explained waving his hand around.
"That's wonderful," Emma spoke up, "Right, Baby?" she asked, turning to look at the toddler. The little boy nodded enthusiastically.
"Yeah!" the smile on the boy was so big that Killian could have been knocked backwards, seeing this child was shocking to him. Where had he come from, whose was he?
"Emma, who is this?" Killian asked apprehensively, had she found someone else, was he farther in her homes as well. Did she truly not wait for him?
Emma paused for a moment in realization that Killian didn't know about Liam. She peered down at the little boy latched onto her side. "This is our son," she said slowly. Killian took a step forward, his eye not leaving the child's.
"This is…" Killian's voiced wavered.
"Liam." Emma's eyes were met with the blue eyes she had missed, she nodded, not missing the fact that Liam had turned to look at her as well. "Liam, that's your Papa."
Killian placed his hand over his mouth and took the rest of his steps over. Both him and Liam reached for each other at the same time and he pressed the tiny child into his chest. "Liam," he whispered, his fingers coming the boy's hair. "My son."
Emma and Henry watched the scene, their first meeting, precious. Killian wrapped an arms around Henry and reach around him to grab Emma, pulling them both into his embrace. He held them tight as if they all might disappear from his life again. "We should go now," he told them. They all pulled back and nodded.
Henry went to pack some belongings, and Killian followed Emma to her room to grab stuff as well. He didn't want to put Liam down, but did sit on the bed with him eventually. He started a casual conversation with Emma, about how she had been the past few years and what happened when they returned to the Enchanted Forest. "You're parent's found out they were with child a few months ago," he told her, "They believe it's another girl."
"That's great, they'll be shocked that I beat them to the punch. "Emma laughed, putting some clothes in her suitcase and brushing her hand through Liam's locks, he had passed out on Killian's shoulder due to be worn out from all the excitement.
"I'm sorry you had to go through that alone, Love." Killian said as he grabbed her hand, "I should have stayed."
"No, it's okay. I told you to go, I didn't think I was pregnant. And when I found out the reason I handled it so well was because I had Henry to help and knew that my family was safe with you. You still eased my mind, even from another world." He pulled her fingertips to his lips, and she gave him a loving grin, "Killian, I love you, and I would do all of it again as long as you found me."
She bent down and pressed her lips against his, they shared a passionate, long-awaited, kiss and only broke it off when Liam began to stir.
"It's been too long, Love." Killian drolled out. Emma smirked at him, and went back to packing.
"Yes, yes it has."