A/N: Based on the idea that the duplicate Doctor wasn't as comfortable with having the Doctor's thoughts and memories as we assumed…
Jonathan Don Noble- 'John' for short- leant against the doorframe of the bedroom, watching Rose sleep. They'd been in Pete's World for little over three weeks now, and he was still getting to grips with being part human. He yawned, and crossed his arms, ignoring how the fabric of his hoodie crinkled beneath the movement; he had stopped wearing suits just a few days after returning from Norway, hysterically insisting that he wanted to be his own person and Rose had soothed him, telling him that he shouldn't feel any obligation to wear suits if he didn't want to, she'd love him anyway. Jonathan still didn't sleep as much as a normal human- although that was out of stubbornness- and had taken to wandering around Rose's apartment while she slept. He couldn't help but smirk as, even in the dim light of the bedroom, he could see the mess strewn across Rose's bedroom floor. She had never been particularly tidy, always insisting that there was no point making her bed if she was just going to sleep in it again several hours later. Shaking his head to clear his thoughts, he finally tore himself away from Rose's bedroom door and headed back to the sitting room.
The next morning, Jonathan and Rose skirted round each other as they prepared their respective breakfasts. Both he and Rose were still a little apprehensive and uncertain about their relationship, but for different reasons; Jonathan understood that it was hard for Rose, trying to work out if he still was the Doctor, if he was the same man she had fallen in love with all those years ago. But he had a different problem. Because, Jonathan Don Noble loved Rose Marion Tyler. He had been born so full of love for a certain pink and yellow human that he had been drawn to her instinctively once they were safe onboard the TARDIS. It had been easy to tell Rose that he loved her, because it was true, and instinctive, and if he only knew one thing, it was that he loved her so, so much. But in that lay a problem; he loved her purely because he was born that way. It wasn't a conscious choice (as much as falling in love ever is) and he hadn't fallen in love with Rose. As much as Jonathan insisted he was the same as the Time Lord Doctor, with the same thoughts and memories and physical attributes, the truth of it was that this body, his body was very much new, and this body hadn't been the one that had fallen in love with Rose Tyler. He couldn't deny his love, because it was very much real, but he couldn't help but feel that he was in love with this woman…Well, out of obligation. And he had no idea what to do about it.
Jonathan spent the next few weeks trying to work out how to break the news to Rose. He'd even packed already, but had yet to bring himself to put his plan into action. He knew he had to, it was driving him mad. He was no longer certain whether he was a free man- whether he'd ever been a free man- or whether everything he'd ever do in his life had already been dictated by the Time Lord Doctor who'd dumped him there with barely a second thought. His memories from before he'd woken up in the TARDIS, stark naked with a wide-eyed Donna in front of him, were clear as crystal in his mind, but it hadn't been this body that had lived them. Did that make them any less real? All the feelings he'd felt when he'd travelled with Rose, Martha, and all the companions before him, were they actually his? And what about his beliefs? Wide-eyed and breathing heavily, Jonathan launched himself from the sofa and virtually ran to Rose's bedroom.
Rose was, of course, asleep as it was little past two in the morning. However, Jonathan was determined to sort this out once and for all, and so hurried into the room and over to the bed, shaking Rose's shoulder forcefully enough to wake her, but not enough to hurt her.
"Jonathan?" Rose mumbled tiredly, rolling over and squinting in the dark.
"Yeah, sorry," he replied quietly, seating himself on the edge of the bed.
"We have a rule about this kinda thing, Jonathan," Rose murmured, rubbing her eyes.
Jonathan's brow crinkled as he tried to work out what Rose meant.
"You're meant to knock on the door," Rose supplied sleepily, forcing herself into a sitting position "but never mind now, what was it you wanted?"
"We need to talk," Jonathan broke in urgently, eyes wide.
"Right…" Rose began cautiously, unsure how to reply "what about?"
Rose blinked at him, before pushing the duvet back.
"Maybe we'll be more comfortable in the sitting room," Rose suggested quietly.
"So, what're you saying?" Rose asked quietly, frowning.
"I…I'm not sure," Jonathan admitted quietly, rubbing the back of his neck.
"What happens to us now? I mean, if I'm understandin' you right, you love me but you're not sure whether it's because of me or because of you havin' the Doctor's thoughts and memories," Rose clarified, biting her lip and suddenly finding her nails extremely interesting.
Jonathan sighed, burying his face in his hands for a few moments before replying.
"I don't know, but I think it's best if I leave for a while. Just until I have everything figured out," he replied.
"But where will you go?" Rose asked, the tears beginning to fall now as she finally met his eyes.
"No idea," the Doctor replied "but then again, when have I ever known where I'm going?"
That drew a watery laugh from Rose, and he smiled slightly at the familiar sound.
"How long will you be gone for?" she asked as they grew serious again.
"As long as it takes."
"An' when are you leavin'?"
"Well, now," he admitted "I figured it'd be best for me to leave after this chat."
"Now?" Rose echoed, glancing at the clock on the wall.
It was only four am. Jonathan nodded. Rose smiled sadly, and nodded back as he stood and headed to the door. His rucksack was already packed with what little possessions he owned and waiting for him underneath the coat hooks. As he swung it onto his shoulder, he offered Rose an awkward smile and pulled her in for a hug, savouring the feel of her body against his. Pulling away, Jonathan looked at her carefully, committing the image of her to his memories; one of the precious few memories of his that this body had actually lived through. Rose looked adorable as she watched him, slightly teary-eyed and bundled in her light blue dressing gown, hair a mess and wearing mismatched socks.
"I guess this is goodbye then, yeah?" she asked quietly, scuffing her feet on the floor.
"Oh, Rose Tyler, I hope not!" he replied, tears beginning to well in his own eyes now.
And with one last wry smile, Jonathan opened the door. All Rose could do was watch as he stepped out of her apartment. For the third time, the Doctor had stepped out of her life. The tears rolled down her cheeks thick and fast, much as they had done just minutes before when they had talked. And unbeknown to Rose Marion Tyler, Jonathan Don Noble stood on the other side of the door and finally allowed his tears to fall.