1.
The Doctor doesn't think of Donna much, which is a blessing. It hurts to think of her, hurts to think that he did the right thing in saving her life and still ended up alone. Like always.
He travels alone for a time, just wandering and looking at stars and occasionally running from things. He eats a lot of bananas, sulkily. Then he meets Fletcher, a young and excitable Coatl with lovely yellow tentacles (turns out that mistaking someone for a banana doesn't necessarily destroy any possibility of friendship) and takes him aboard the TARDIS, who immediately obliges the new guest with rooms full of warm pools that the Doctor had nearly forgotten about. They have fun together. He's okay.
Eventually Fletcher settles down with a lovely, spiky Octopodrone and the Doctor goes on alone again for a while. He doesn't feel so sulky now; he's maybe even a bit hopeful. He dances to the beat of the twenty-seven-headed drum of Bandoorah under the light of the planet's twenty seven twinkly, purple stars; he bathes in the waters of Qundravium Three and has to pick nits out of his hair for days afterwards.
Then he lands on a nice, peaceful planet, populated with things like sloths that speak only in colors. It ought to be relaxing, but when he tries to make a joke about rhyming with orange, all of a sudden they're chasing him through the trees (not that much like sloths, apparently) and one of them grabs a hold of his leg, and…
The regeneration goes wrong somehow. He can feel the energy shuttling along his nerves, refusing to dissipate. He makes it back to the TARDIS, but only just has the strength to flip the lever for Emergency Protocol Two (nearest sentient and sensible person who can reliably be counted on to make a cup of tea) before he collapses. The TARDIS rushes through space and time, and it's only a few moments before they land. The Doctor staggers out of the ship, right into Donna Noble's arms.
"Er," he says, and passes out.
The next few days are a feverish haze as the light of the regeneration energy sizzles behind his eyelids in intricate patterns. The sound of the light is a mocking howl as shivers sweep over him. Sometimes, dimly, he can feel a damp cloth on his forehead and cool fingers in his hair, but that's all he knows.
He wakes on the third day and Donna is asleep in the chair beside the bed. She looks older, more worn, but still Donna. His leg twitches and the rustle of the sheet is enough to wake her. As her eyes open, she gives the Doctor a sleepy smile, and he can't help but smile back. Then she comes fully awake and smacks him on the head.
"Ow!" he protests.
"You deserve a worse one," she says, "but as you're still a bit sick I'll go easy on you."
"But Doooooonna," he whines. She thwaps him again, not quite gently.
"That's for underestimating me." Then she leans down and wraps her arms around him. "Don't let it happen again. I'm glad you're all right."
The Doctor holds her for a long moment, looks her right in the eyes when she pulls back. He can see himself in there still, can see the genius of the Time Lord mind like a light shining from inside. But most of what he sees is Donna Noble, and it appears that she hasn't lost her ability to push a Time Lord around, even when she doesn't get to use her right hook.
She's right; he'd underestimated her. It's a good thing, he thinks, that she's so bloody brilliant.
"I love the new look, by the way," she says. "Very flattering."
"New—ooh!" he says. "Am I ginger? Haven't even had a chance to look at myself yet!"
"Are you ginger?!" she says incredulously. "You ain't half." She gets up to fetch the mirror, and in a minute there are two redheads staring back at him.
The Doctor throws back his brand new head and laughs.
2.
"Run, Spaceboy!" the Doctor hears, and both of his hearts seize up. He turns, and there she is, ginger hair flying behind her as she crosses the courtyard of the Cravalaxian palance.
"Donna!" he says, absolutely flabbergasted (great word, flabbergasted, he thinks).
"Oi," she says as she pulls level, "were you always this bad at following directions? Run already!"
A pair of guards appears at the corner and the Doctor suddenly sees the wisdom of her plan. They run. Donna can run as fast as he does, now, and he doesn't know why that's the weirdest thing to strike him about this situation. He ought to save his breath, but he can't help himself.
"But… you…" he says. They duck through a doorway and a thought occurs. Maybe it's a timeline thing, maybe she took a side trip while they were traveling together and that's all this is. It's a pretty depressing thought. "Remind me," he pants, "when was the last time you saw me?"
She gives him a look. "When you dropped me off. Without any memories or so much as a backward look."
"That's not true," he says before he thinks about it, then clamps his mouth shut. Out of the corner of his eye, he can see her face soften a little bit.
"But how are you—" the Doctor says, and then Donna pulls him into a darkened room off to one side of the hallway. A few seconds later he can hear the guards run past.
"How am I here, flyin' about the bloody universe? Is that what you want to know?" whispers Donna tartly.
"How are you alive?" he whispers back, and he can feel the grin spread over his face like wildfire. He grips her by the shoulders there in the dark just to know she's still there. "Donna Noble, how are you alive?"
Before she can answer there's a banging on the door and they have to climb out the window into some decidedly unpleasant-smelling bushes. The guards follow. They run some more, trading the safety of the castle's shield bubble for the rough air of the planet's surface.
The Doctor can feel his grin widen as the wind whips through his hair.
"Well?" he hollers. Donna turns to look at him, and a flush spreads over her. She has to shout to be heard over the wind, and at first the Doctor only catches one word in three.
"Jack… side effect… Ianto, too, which is quite…" She makes a gesture with one hand.
The Doctor's eyes widen involuntarily and she moves close enough to shout in his ear.
"Honestly, I really think you'd rather not know!" He nods.
3.
It isn't until the skinny bloke is gone that Donna starts hearing the voice. At first it's just a whisper of rain outside the window, distortion on the line as she's listening to Nerys tell one of her standard tall tales.
But soon the rain is calling her name, and Nerys is drowned out by a man's voice, like two lines crossed, two conversations happening at once. The voice is weeping.
"I'm so sorry, Donna. So very sorry."
"Who are you?" Donna whispers, and a flash of memory comes to her. There's a man in a suit, skinny and with a mouth slightly too full of his teeth. He's crouched outside a window and he's looking across the room at her, giving a jaunty wave.
"You left me," she says. The memories are rushing back now. "You left me."
"I'm sorry," says the voice. "But I wasn't ready then. It wasn't time yet."
"But it is now," says Donna. There's a weight in her pocket that wasn't there before, and she slides a hand in to touch the too-warm metal, the elliptical curves and symbols carved into its surface.
"Yes," says the voice. "It's time now."
"I'm gonna be with you forever," says Donna, and opens the watch.