Learn to Fly
He touched her, and she sang.
Oh, not at first. Not really, anyway—but she needed and he needed, and together, they made a fit. Not a perfect fit, of course, but a fit all the same. She was a TARDIS waiting for destruction. He was a Time Lord with nothing and no one to hold him down.
It was a fit.
He told no one of his plans, not even Susan. He didn't mention to her that he'd snuck down to the breakers on a whim and had been shocked to find her doors open and waiting for him. She was calling, that old and not-quite-yet-obsolete TARDIS, crying out for someone, anyone, to make her their own. She'd never had just one pilot, had never bonded with a single Time Lord: her life had been as a taxi of sorts, transporting groups of Time Lords or students to where they needed to go. Now she was old, replaced by a newer model.
Yet she'd always been wanting. Stretching. Needing.
Hardly meaning to, he had stepped inside. Touched her, and been welcomed by a brilliant if difficult song—not one promising of glory or perfection, but one that fit, all the same. He was obstinate; she was ornery. He was fed up; she pled for freedom.
Maybe they both took their pains out on one another. Maybe it took him years to fully accept what she meant to him, and he to her. He'd not been prepared, really. Hadn't intended to bond with a TARDIS, to give her a corner of his stubborn and rebel soul. But she'd expected him to, so from the beginning, they'd had problems.
Beneath all that, though, they'd had something in common. From the moment he grabbed Susan's hand and asked her "Do you want to see the universe?" he and the TARDIS had both yearned for the freedom of the cosmos, for more than they could find on mere Gallifrey. After all, what was there to hold them still? She awaited physical destruction. He was spiraling towards destruction of another sort, of the inability to put up with the stuffy superiority and condensation one moment longer. Either way, they'd both been ready for something new.
Susan had gasped when he'd shown her the creaky and old (and beautiful and brilliant) machine who had agreed to seek out adventure with them. Susan, lovely Susan, had seen the beauty immediately, even if she'd been a bit doubtful that her Grandfather had found a safe mode of transportation—or if he'd perhaps gone crazy and was looking for disaster.
Truth be told, they found disaster as often as they found adventure, never quite sure where they'd end up. Oh, the Doctor was often pleased by the sheer randomness of their adventuring—so different from stodgy, orderly Gallifrey—but he'd been frustrated that the TARDIS simply refused to accept his directions. He'd hated her, for a time.
Years passed before he understood that one couldn't really pilot a TARDIS like this one. You had to fly.
Pulling out the manual didn't help, even when he'd finally (grudgingly) bothered to do so. Hitting the right buttons and levers only did some good; the TARDIS still traveled where she wished, when she wished. She was alive and wanting, and he was blockheaded and terrified of answering that need he could feel in his mind.
Still more years passed before he dared let his barriers down and she became his TARDIS. Old, out of date, and ornery as she was, she became his.
He became hers. Her Time Lord.
Decades more passed before he could reliably direct her at all—even when she was feeling kind, his TARDIS had a mischievous streak a hundred parsecs wide. And so did he. They fit well together, after all. Had from the beginning.
Susan left before the transition occurred. So did so many others…except the TARDIS. Perhaps the final realization that they would all leave did him in, made him open up to the one constant companion. She would never leave him, he realized. Never find herself another Time Lord. When his final moments arrived, she'd be there with him, physically or in his mind. And when he died, she would as well.
No breakers this time. She wouldn't have to wait for destruction. When the Doctor died, the TARDIS would follow him. She'd never promised him that, but she never had to. He knew.
He was her Time Lord when he spent ten years dying alone in the TARDIS, in pain and so terribly lonely. He would have gone mad if not for her constant presence, for her love and her embrace.
She was his TARDIS when she willingly put herself in the midst of battle and death and danger, helping him do the one thing they'd been sure would kill them both.
They were together when he woke up, hours later. He'd expected to die, wanted to die, and so had she. But they'd found, together, that they'd been saved for a worse destiny: to live and to be the last of their kinds, fighting when and where they could.
They were millions of years apart when she opened her heart up to a simple human girl, because the TARDIS was desperate to get back to her Doctor, desperate to save him, even from himself.
She was all he had when everyone else left, and he sat, drenched by rain and tears, cold and lonely yet again. But her presence was warm in his mind, and when he touched the controls, eventually he remembered that she had taught him how to fly.