It was night time in the TARDIS. The Doctor looked into Rose's room to ensure she was sleeping peacefully. The room's walls were lined with soft toys and the time lord couldn't help but smile when he saw that there wasn't a single toy on the girls bed.
Next he checked on Jack. The captain's room was bare, his sonic blaster being the only visible personal effect. Despite this, however, Jack had an extra pillow on his bed and was cuddling it as a child would a teddy bear. Grinning the Doctor decided to get him a soft toy.
Jack frowned when he entered his room in the TARDIS, during a trip to Earth, to find a teddy bear sitting where his spare pillow used to. Picking it up he headed to ask Rose if it was hers. It wasn't. Shrugging he asked if the Doctor knew where it came from. The time lord just grinned at him, telling him to keep it.
When the Doctor looked into Jack's room that night the captain was hugging the bear like he had the pillow.
"You gonna kiss me goodnight?" Jack mumbled sleepily.
"Buy me a drink," the Doctor grinned, leaving.
The next day Jack bought the Doctor a drink. Grinning the time lord wrapped an arm around the captain's shoulders and led Jack back to the TARDIS. Outside he drew Jack in for a deep kiss before heading inside. Smiling Jack followed and headed to bed.
Later that night, as he did every night, the time lord looked in on Rose and then Jack. Rose was sleeping peacefully but Jack was clinging to his teddy bear and moving restlessly. The Doctor crossed the distance to the younger man and climbed onto the bed behind him, wrapping him in a comforting embrace.
This soon became the time lord's reglar routine; checking on Rose before climbing into bed with and simply holding Jack. Gradually their relationship began to progress. It started one night with Jack sleepily kissing the Doctor and then other stolen kisses and gropes.
Barely a month after the time lord crawled into bed with Jack the captain straddled him and slipped a hand down his trousers. The Doctor immediately responded and soon both were naked. They began moving together until the Doctor flipped them and entered Jack with a single thrust. They came together and feell into a contented sleep.
When Ianto entered the hub he saw Jack was still asleep, cuddling his pillow, like most mornings. Since he had lost Lisa he had become good friends with the captain and watching Jack sleep he decided to get his friend a present. Slipping back out of the hub he returned several minutes later with a small stuffed bear.
Jack stared wide-eyed at the bear when Ianto handed it to him. Without realising it a single solitary tear rolled down his cheek. Ianto quickly hid the bear and apologised. Jack shook his head morosely and they never spoke about the bear again.
When Jack returned to the TARDIS he went straight to his room, picked up his bear, and cried. His Rosie was gone, replaced by this Martha, his Doctor was gone, and his lover was gone, replaced by a stranger. The time lord knocked quietly and entered the captain's room.
"He's not gone, you know. He and I are the same person, I feel the same for you as I always did," he claimed. "I love you."
Jack sobbed and buried his head in the Doctor's shoulder, crying. He cried himself to sleep and the time lord continued to hold him.
Jack and the Doctor's relationship progressed slowly. The Doctor explained that the captain's immortality was linked to the time lord and the TARDIS meaning he would live until the Doctor died. Martha was oblivious to their relationship and the time lord spent every night holding Jack and allowing the captain to to take things at his own speed.
The time lord was sitting on Jack's bed when the captain crawled onto his lap. They proceeded from there, quickly dispensing clothes. The Doctor took things slower than he had their first time, penetrating Jack first with his fingers and then his cock.
"I want to go home."
Jack looked up at Martha's statement. He had known she wasn't completely happy; she had feelings for the time lord that weren't reciprocated. The Doctor frowned but agreed.
Unfortunately they crashed in Cardiff. Martha decided to travel to London the conventional way and quickly left. Establishing that the TARDIS simply needed to recharge the time lord took Jack out for lunch. They didn't expect to meet the Torchwood team. Jack, unable to take the betrayed look on Ianto's face, returned to the TARDIS. That night the Doctor simply held Jack comfortingly as he slept.