The Darkness within
It had been a standing joke amongst those at the Academy that 'the Doctor' was as aberrant and unpredictable as the time they were attempting to understand, and even more unfathomable to the rest of the Time Lords in training.
His colleagues mocked his interest in all things inferior, ridiculed his unbridled enthusiasm for lesser species and scorned his compassion. His naivety was a source of great amusement; his heritage a basis for derision and his attitude a foundation for disapproval. His fellow students found his eccentricities to be amusing, his lecturers found it infuriating.
But they all agreed on one thing; the Doctor would not have an easy time in life.
In typical Gallifreyan fashion, their assessment of the situation was 100 correct.
Rejected, exiled and ostracised before his four hundredth birthday, and practically running through his regenerations like water sliding through his fingers, discarded with a carelessness that emphasized his distain for the society that sought to restrict him, the Doctor would never live up to the Gallifreyan standard of a Time Lord.
Whether rumours of a human mother were true, whether talk of faulty looming were accurate, or if the gossip of recessive genes and time radioactivity were correct, it didn't change the fact that the Doctor was flawed.
Most Time Lord regenerations went smoothly, the Time Lord— or Lady— in question, sliding effortlessly into a new form, choosing carefully what body or species to spend the next few hundred years in. They didn't wait until the body was almost wrecked, with barely enough energy to regenerate a few years younger; they ensured that they would have at least as long in the next body as they did in the current one.
The Doctor, however, allowed his first form to age practically to pieces before regenerating, making his second body only marginally younger. The enforced regeneration of his second incarnation, again, allowed him only years instead of decades of respite in his next form. He still harboured resentment at being thrust into an unwilling regeneration by the Council due to his "crime" of interference in alien matters and his third form bore that grudge with dignity and grace.
The Doctor held true to this pattern throughout the years, and each of his regenerations was more painful and less stable than the last, until, finally, it all went so very, very wrong.
To be perfectly fair, it wasn't entirely his fault; after all no Time Lord in all of time would ever expect to have to hold all of the Time Vortex within his fragile form.
The process had never taken into account any latent death wish, or the extinction of a species or even the obsession of one man with a single human child.
During his excruciating change the ninth incarnation of the Doctor held on to one thought and one thought only, that of the girl standing horrified in front of him.
His Rose, the girl who had taken his hand and taught him how to live again. The girl he had fallen hard for and could never tell because he was too damaged, too ravaged to be allowed to hold onto such innocence. He loved Rose Tyler with all his hearts and in the last moment his thoughts were not on his next form, or on the threat of the Dalek invasion force she had just eradicated from space and time, nor were his thoughts on his ship or the pain he was in. Every single last neuron was wholly focussed on her— hoping she could deal with the next him, hoping she would stay with him, and, in his final seconds, wishing he did not have to leave her.
The Time Vortex had granted life, it had rearranged matter and divided atoms and ended a war that destroyed civilisations and spanned millennia.
To grant one last wish was nothing.
So as each cell died and was reborn, shuffling its genetic code into a new variation on an old theme, parts of the man tenaciously held on refusing to be dispersed.
Parts of the war-wounded man with a bitter spirit tempered by Rose-coloured hope, refused the process with a single-minded focus and, using the Vortex, planted himself as a separate entity inside his new incarnation, dormant, but observing and aware.
Immediately, the new Doctor knew that something had gone wrong. He still felt everything for the girl in front of him that he had before, he remembered everything, he understood everything and there was a part of his mind that he could not access.
He didn't have time then or later to think on it as threats arose and danger lurked, and he was thrust into his new life with gusto and a healthy dosing of caffeine and sugared tannins.
He forgot about the piece of his brain that eluded him and babbled to cover his confusion when something inside mocked him for his exuberance.
The surge of anger in his mind when Rose was in trouble made him giddy and he was far fiercer than he had any right to be. He found himself saying things, or almost professing feelings that he never would have thought of, let alone said, and he found his actions contradicting each other with an almost alarming frequency.
Even as he smiled at a French courtesan his head was screaming at him for leaving Rose behind and, despite his despair at losing his TARDIS, he couldn't help radiating abashed pleasure when Rose indicted her willingness to live with him.
The Doctor had taken his apparent madness as a matter of course, simply a different wiring for a new incarnation, but it wasn't until the doors closed on a not-too-blushing bride that he realised exactly how wrong things had gone.