A/N: I ran out of steam with this, but here is the ending.
"Re-what?!" Peter spluttered. "What the fucking hell is that?"
"Regenerated," the Doctor repeated. "It's our way of living longer. Every cell is renewed, leaving only the memories. The face can change and the personality along with it."
"Like an upgrade," Peter tried to reason. "So you've done this yourself?"
The Doctor nodded. "Nine times now. Each time is painful and disorientating."
"Why didn't Mum change in looks?" Peter wondered; quite logically in the circumstances.
"I'm not sure," the Doctor admitted, "probably due to her being only part Gallifreyan."
"Does this mean that I will regenerate?" Peter asked, keeping his eyes on Donna.
"Oh, more than likely. If Donna can do it then you should be able to easily," the Doctor answered. "You might actually change appearance."
"Why would I want to change this?" Peter then asked as he stroked his chin. "I'm very fond of these looks."
The Doctor chuckled. "I felt that way too. That's why you exist… well, sort of."
"You needn't have shagged Mum," Peter put in.
An immediate blush appeared on the Doctor's cheeks. "Yes… well… I erm…"
Peter grinned knowingly. "Did you actually fancy Mum? I mean, seriously? I thought you were only acting for the sake of the timelines."
"I'll have you know that your mother is a very desirable woman!" the Doctor defended both himself and Donna. "We were in love, but it wasn't meant to be; so I did the right thing."
"By running off without a word," Peter said calmly and sarcastically. "I'm sure we'll be eternally grateful."
The Doctor drew in a sharp breath. "Peter, it wasn't like that. I had to think of the bigger picture, and I knew that I would meet your mother later as a friend. I couldn't ruin that with talk about how I felt."
Peter didn't really know what he felt, as he stood taking in his father's sad expression, beyond bitterness. "Then why touch her in the first place?"
The Doctor looked even more defeated. "I've often asked myself that same question. What was I to do? I had wanted her so much before that day. She was so beautiful, we were having fun together, and it seemed like the most natural thing in the world until Martha came home."
"Don't tell me anymore," Peter insisted, holding up his hand. He went to say another thing but a small movement caught their attention.
The Doctor was ahead of Peter by her side as Donna flickered open her eyes and saw him for the first time in what felt like decades but was six years. "Spaceman? Do you remember me?" she asked hoarsely. "What happened?"
Her eyes then travelled to the man so awestruck to her other side when he gasped in a sob. "It can't be… Is it? Earthman, is it you?"
"It's me, Mum," Peter said tearfully, instantly wondering who Earthman is.
"Peter? My Peter? My baby boy, all grown up?" she cautiously asked as she tried to reach out to him.
He caught her hand and hugged it to his cheek. "Yeah," he answered, unable to say more.
"You're so handsome," she stated, and started to tremble with emotion. With effort, she brought up her other hand to explore his features, tracing his cheeks, lips and jaw. "My Bunnikins," she sighed as tears overwhelmed her. "I thought he would kill you."
"No, I'm still here," he replied, smiling reassuringly through his tears.
"I bet you could do with a decent cup of tea," the Doctor remarked.
"Would I?" she readily agreed. "I'm spitting feathers here."
The Doctor bustled away to the kitchen to keep up a necessary supply of tea; it always felt good to have plenty of tasks to carry out, and it distracted him from the emotion of the reunion scene he had just witnessed.
As he carried back their mugs of tea to the medbay he resolved to help Peter mas much as it was within his power to. That meant starting with a bedroom especially for him, and then supplying the process for Peter to heal wounds that were just as fatal as Donna's had been. If he could sneak away, he considered a visit to Ray Vincent before he closed the book on this chapter of their lives. The Doctor's thoughts ran along very dark lines as he ran through his head all the clues Peter had been dropping, and he didn't like the conclusion one bit. But first Donna needed tea, and lots of it, to fight off her regeneration sickness.
A relatively short while later, the Doctor laid his hand on the head of Peter as he slept, leaned forward and kissed his forehead. "Sleep well, my son," he said to the sleeping form, raised his hand to touch the wall above him, causing the lights to dim right down and a chill filled the air. Satisfied that things were as they should be, he left the room.
Next was a slight detour.
The Doctor waited until Peter was convincingly out of the way before heading to where Donna sat comfortably with a cup of refreshing tea.
"Donna, I need to explain," he immediately tried to say as he sat himself down by her chair.
She held up her hand to halt his words. "No need to, Spaceman. You have nothing to apologise for, I know that now."
His sad expression said it all. "But about what happened back in 1969…"
There was a wave of her hand to dismiss it. "It was yet another one night stand in my life. I should have known better."
"The photo, Donna!" he protested. "Peter showed me the photo you carried about with you."
"Ah," she said guilty. "I'm sorry you had to learn about it. I promise all that has finished." There was a snort of derision. "I won't need to now that Ray is dead. Who'd have thought I'd be grateful for the actions of a vampire?" she wondered, not looking at him directly. It was only then that she fully contemplated him. "I assume this is it, the time you drop me off for good and wend your way to the next adventure. I don't suppose you want to help explain who Peter is for me…? No, of course you don't."
He struck out a hand to stop her from getting up and walking away from him. "Donna, are you going to let me get a word in?"
"I know the word won't be 'goodbye' but it'll mean the same any way; so let's not drag this out any longer than we need to," she answered.
"You're being very cold about this," he retorted.
She sighed. "I'm being a realist. I've had a long time to get over you in one form or another, and although I've just ruined things by becoming even more like you I know when to cut my losses." There was a hint of a smile when she added, "I got what I wanted: my son to be safe. I'm not risking anything further than that."
"And what about me, Donna? What about what I want?" he softly asked.
"You? I'm sorry but I didn't know I had to provide more than I have. I can't give you back Rose, and you'll have to excuse me for feeling bitter that you gave away D2 to her; only I technically haven't had long to process it," she remarked. There was probably something else she should be aware of but her mind was still feeling decidedly woozy after the effort of regenerating.
A choked sob wrenched its way out of his throat. "I thought you understood."
"No I don't. In fact I'd appreciate it if you'd tell me why you banged on and on about loving someone, she rips apart several universes to get back to you and then you dump her with my D2," she raged at him. "Although you had the cheek to do all that after knocking me up; so much for deep everlasting love," she added scornfully. "It sounds more like you were in love with the idea of love."
"I didn't knock you up, as you so charmingly put it," he commented.
"Oh yeah? Well it wasn't a special gift from Father Christmas before you try to deny it again!" She was absolutely fuming now. How dare he! "Or are you playing semantics?"
He had to think about that one. "Semantics does come into it; but you were already pregnant when I… when we er…."
She placed her hand over her eyes in exasperation. "Oh dear! He can't even say the words, it's that abhorrent to him," she said to nobody in particular. Her hand was lowered so that she could glare at him openly. "Well?"
The Doctor nervously gulped. "The metacrisis also backfired by creating a second duplicate with the missing heart. You were pregnant but dormant until the Weeping Angels and I helped things along."
"How did you help exactly?" she wanted to know.
"I er… provided some growing medium, that aided development," he admitted. "And not in the way I thought I was supposed to."
"That must have been a shock for you," she agreed. "What would have happened if you hadn't?"
"The baby would have died soon after birth," he hesitantly answered, and took her hands when she gasped in shock. "It was an essential part of development when my species actually mated."
Her mouth tried to form the question, "So… Peter is…?"
"Almost completely Gallifreyan," he supplied; rather proudly, in her opinion.
The Doctor then glanced hesitantly towards the doorway. "What's up, Doctor?" Donna immediately asked.
"I found something outside the door earlier," he said as he got up and made his way over the medbay door. "Judging by what I saw earlier, I think you might be more than a little interested to see." Opening it, he bent down and picked something small up; it looked remarkably like…
"Peter!" Donna gasped out in shock.
The boy within the Doctor's arms stirred from his deep sleep, rubbed his eyes, and peered at the Doctor inquisitively. "Am I dead?" he asked the Doctor.
"Erm… sort of," the Doctor answered vaguely.
"Is this heaven," young Peter then asked.
"I hope so," the Doctor said with a smile. "I tend to think of it like that."
"Are you my dad?" Peter then risked asking.
The Doctor's smile grew broader. "Yes, Peter. And I know you have the photo of me to prove it."
There was an equally dazzling smile in reply. "If this is heaven, where's my m-," Peter started to finally ask as his eyes began to explore the room. "Mum!" he squealed in delight, and bounced with joy. "You found my mum!"
Without any hesitation, the Doctor took him straight to Donna's waiting arms. "Oh my Bunnikins," she crooned as she kissed his little head and felt him cling to her as he sat on her lap. "What about older Peter?" she anxiously asked the Doctor.
"He's in stasis, sleeping until the reality he likes occurs," he replied. "Don't worry, love, he wanted this; he wanted me to rescue him." The Doctor then affectionately wiped away some of her tears. "Typical Donna Noble! Another whole parallel universe created, just for you," he teased. "One that I'm beginning to like quite a lot."
She accepted his brief kiss. "Thank you, Spaceman."
The Doctor knew it would take her time to completely trust him again, but he didn't mind. This was a fresh start for them all, and he'd had a heck of a lot worse. Here was a start where he could look forward to the next chapter; and he wanted to savour every moment.