Disclaimer: I don't own Doctor Who.
NOTE: To understand this, I created a character, Patrick, a few months ago. He is supposed to be Jamie and the Doctor's son (which is why to him the Doctor is "Daddy" and Jamie is "Papa", the name for the female companion depended on which girl it was ("Mama" for Victoria, "Mommy" for Zoe)) and... well... the reason why he is not around should be pretty obvious after you read this.
WARNING: The Doctor may or may not be terribly OOC in this.
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Patrick bolted upright in bed, panting heavily and quivering. He'd had a bad dream and didn't know if he was currently in reality or not. Once his blurred vision returned to normal, he decided he was back in the real world and tried to compose himself. When he could not, he decided to go find either Jamie or the Doctor.
Slowly, he crept down the TARDIS' corridor to first check Jamie's room. Sometimes they were in there, other times they weren't. This was one of the latter times. As he made his way to the Doctor's room, he listened intently to the ship's soft humming. It was calming, almost soothing, and by the time he reached the door to the Doctor's quarters he was trying to resist the urge to just return to his room but then the whole trip would have been for naught.
"Daddy?" Patrick carefully poked the lump hiding on the bed underneath the comforter. It shifted and a knee suddenly poked out, clothed in the Doctor's pajama bottoms, but the unintelligble grunt that came immediately afterward proved to be just Jamie.
"Patrick, what are you doing up?" a voice whispered. The toddler looked to the other end of the room where he saw the Doctor in his study, oddly dressed in Jamie's pajamas. (This was a ritual Patrick was sure he would not understand until he was older, his fathers switching pajamas in the middle of the night.) He ambled towards the Time Lord, slowly and carefully closing the door behind him so their conversation didn't wake Jamie.
"Daddy, I had a bad dream," Patrick explained when he was situated on the desk so they were nearly eye-to-eye.
The Doctor furrowed his brow, deeply concerned. The boy had not once had a nightmare before-the near-constant conditions made that almost illogical. He stared deep into the changing, multi-colored eyes, trying to identify what could have caused a panic.
"What happened in it?" The tone of the Doctor's voice showed he had shifted gears from cosmic hobo to protective father.
"We-meaning me, you, Papa, and Mommy of course-landed in the time of the first World War and eventually you noticed all different kinds of wars going on at the same time. And you contacted your people and they returned everyone but they put you and another man on trial and..." Patrick choked. The tears that had started forming in his eyes fell.
"And what, Patrick?" the Doctor said, the hair on the back of his neck standing on end. "What happened after another man and I were put on trial?"
"We were sep... sep..." The boy could no longer hold back his cries.
The Doctor wrapped his arms around him, muttering words of comfort. Patrick didn't need to finish because the time traveler knew exactly what he was going to say.
"Look at me," the Doctor said. The child did as told and was rewarded with his eyes being wiped with the hem of Jamie's pajama shirt. "I would never let the Time Lords take you or Jamie or Zoe away and if they tried, there would be a big fight. Understand?" Patrick nodded, hiccuping. "There's a good lad. Why don't you go hop into my bed next to Jamie and I'll be there in a few minutes?"
"Daddy, before I do that... what are the Time Lords like? Are they like you?"
A small smile crossed the Doctor's face, showing, unbeknowest to Patrick, how much the man wished it were true.