It started out slowly with the Doctor disappearing to retrieve the key to the warehouse from Jack's office. He never stayed away long at first, only an hour or two but that hour eventually turned into a day and a day into a week leaving Jack to care for the infant on his own. He never had excuses for his absence and he always returned to the home they shared climbing into Jack's bed as if nothing had happened. It angered Jack and he regretted the fact that he took his anger out on the Doctor's body, using him as if he were nothing but a toy for his release. He knew the pain he was causing the Doctor but he hardened his heart against that pain as they continued to drift slowly apart.
As the first year of Emily's life came to pass, Jack was there for all her milestones. He was there as she rolled over for the first time and began to crawl. She took her first steps before she was a year holding tightly onto her encouraging Uncle's fingers as she toddled unsteadily. He was there during the long nights when she cried in sickness and also there for the nights where he would just cuddle her in his arms as she drifted off to sleep. The Doctor came and went and while Emily knew him she didn't look for him the way she did for Jack at first.
"Ja," Emily would coo happily when her uncle came to pick her up from daycare or retrieve her from her nap. Her first words would be a slurred version of his name and it would take several more weeks before she attempted the word that the Doctor so longed to hear. Jack never told him that the first time he heard the word daddy it was directed towards him after a day at the park. She had been tired with her head resting on his shoulder after a long day of running. He heard the word in a sigh as she gripped his shirt tightly. His heart ached for it to be true but he knew that one word wasn't his to claim.
"He will be back soon, baby," Jack had reassured her. The next time the Doctor returned, Jack had been colder than normal to him and after a night of rough sex that left both of them sore, he disappeared for almost a month. It was the longest that he had ever stayed away as they both needed the time apart. Upon his return, he didn't apologize for his absence and neither one of them spoke of the night that happened a month prior but Jack never used his body as roughly again.
By the age of two, Emily knew who her daddy was and Jack could see the excitement in her eyes as the familiar thrum filled the home. She never understood why he couldn't stay and it was Jack who had to deal with the tears of him leaving. Who had to hold the child as she cried for her daddy and acted out in her anger of his absence. Still, Jack held onto her tightly as he swore that he would never hurt her the way the Doctor had. That he would always be there for her no matter what and he would use any resource he had to make sure she was always safe. She was too little to understand how much he cared for her and he never voiced it out loud beyond the words I love you.
Her third birthday was once again celebrated without her father. Only this time she noticed that he wasn't there. He hadn't been there for the first two birthdays either-even if he always made an appearance at Christmas. Jack couldn't tell her why he stayed away as he didn't understand it himself. All he could do was hold his daughter as she cried once again because she felt her daddy didn't love her. It broke Jack's heart but it still took time before he swore that he would never let the Doctor hurt her again, even if that meant hiding his daughter from him. A promise that he hoped that he never had to keep and as the day of the Master's demise approached a part of him was beginning to believe that he wouldn't have to. That this time the Doctor would finally stay.