A/N: I've read a couple of stories with everyone blaming the Doctor for Jack's misfortunes. I wanted to give the Doctor a chance to explain himself better.
Disclaimer: If I owned Doctor Who... well I don't, so there's no point pretending I do.
They had a long day ahead of them, and Martha was getting all the sleep she could. Not too far away, the Doctor was tinkering with some equipment while Jack tried to contact his team once again. Every so often, Jack would awkwardly glance up at the Doctor before turning back to the laptop. The Doctor, for his part, never once looked away from his work and appeared to be attempting to ignore the immortal being near him.
Finally, Jack could take no more. "Doctor," he started. There was no response. "Doctor, please. We barely talked earlier, and now you haven't said two words to me all day. I need to understand." The Doctor steadfastly continued his work. Suddenly furious, Jack lunged forward and grabbed the Doctor's wrist. Perhaps he could force him to pay attention.
The reaction was instantaneous. The Doctor flinched away but not hard enough to break Jack's grip. The Time Lord turned to glare at the human, but even as he did so, the glare quickly turned into a grimace. "Jack," he said as evenly as he could, "please release my hand." Despite the attempt at a level tone, Jack could detect a large amount of stress in the Doctor's voice. Startled, he let go.
The Doctor shuffled back, as far away from Jack as possible while still staying in the light of the small lantern they had set up. He was clasping his wrist to his chest and breathing heavily, nostrils flared. His eyebrows twitched together and he shut his eyes tightly. His jaw muscles bulged as he clenched his teeth. Jack blinked several times, confused. "Are you okay?" he asked softly.
The Doctor took another few breaths and nodded. His eyes opened and he relaxed, but he refused to look at Jack. "You're right," he admitted, "you do need to understand. At the end of the universe, the fabric of space and time was mostly unraveled. My senses were severely limited, and I still felt it. But it was limited, so I was able to deal with it."
"And now?" Jack asked.
"Just looking at you feels like I'm being stabbed in the eyes. Being near you makes my stomach turn. Physical touch… it burns. You're wrong, Jack; you're a fact, and I can feel it, and everything about you literally makes me ill." The Doctor sighed, looking downcast. Truth be told, he felt awful about what he was saying. Jack was his friend, and he hated to harm his friend thusly.
"I'm sorry," said Jack.
"It's not your fault…"
"No, but that hug earlier," Jack cut the Doctor off. "If I had known it would hurt you…" he trailed off.
"You didn't know, and besides, as I said, space and time were all wonky anyway, it wasn't as bad." The Doctor inhaled deeply and shot a glance at Jack. He winced, but continued looking. "I think, Jack, with time, I might be able to accustom myself to your presence, but it will take a while."
Jack grinned sadly. "Doctor, on Satellite 5, when you left me…"
"You did nothing wrong, Jack."
"But you still left me."
"And I cannot tell you how sorry I am for that. What I did was wrong, and I can never make it up to you. I can only apologize and continue apologizing until maybe one day you'll accept." The Doctor ran his hand through his hair, causing it to stick up in several gravity defying directions. "Truth be told, I was not exactly stable at the time. A Time Lord is most vulnerable right before and right after regeneration, and this one was rough. I went a little bit crazy. At the time, I was afraid that confronting you, such a warping factor of space and time would cause me to lose myself. Thinking back on it, with the mental strain I was under, it very well might have. I don't tell you this so you'll forgive me, Jack. I just want you to understand. You deserve that much at least. I also want you to know that I will search for a way to help you."
Jack nodded and smiled tightly at the Doctor. He appeared satisfied, because he soon turned back to his laptop. The Doctor sighed inaudibly. Jack was not okay yet, and he blamed himself. If only he had looked for Jack, had owned up to his faults, had not left him… but that mentality would lead him nowhere. With time, perhaps, the rift in their friendship would heal.
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