A/N: Not seen any episode past the special "End of Time" so please bear this in mind when reading. Don't like Matt Smith as the Doctor so the Eleventh will not really be mentioned.
When the Time Lords made the first TARDIS they revelled in their creation. The ability to move through time and space gave them an advantage which allowed them to become the policeman of the universe. However, what none but a handful of the Time Lords knew was the secret that lay at the heart of each TARDIS. For the select few, who knew the secret, understood that should the truth ever become known, the universe would demand the immediate destruction of every TARDIS. The secret, that they would take with them to the grave, was that at the heart of each TARDIS was the life energy of a Time Lord. The creation of the TARDIS has been an accident, a tragedy that had resulted in the death of one of the Time Lords working on the project. The others only realised what had happened when they tried to replicate the results and failed over and over again. And so, with a willing sacrifice, they replicated the explosion and were stunned to find that a new TARDIS heart was born, while the body of the life energy simply fell to dust.
When the Time Lord known as The Doctor stole a TARDIS from Gallifrey, the life energy that rested within it became attached to her thief. With each incarnation, she grew more attached to her lone pilot, taking him where she thought he was needed. As decades became centuries, she grew more sorrowful, for she knew that each incarnation would eventually die. And all the while she felt her own 'kind' falling to dust, their hearts extinguished as their pilots died in the Time War. One by one, each TARDIS fell until there was only one remaining, and she wept for the ones who had passed before and would never return. But deep within her heart, she too held a secret... One that not even the Time Lords knew... As each TARDIS died, the final spark at its heart was released into the space/time vortex, to become a new life somewhere else. Most returned to Gallifrey, to be reborn as new Time Lords, but some found their way to other planets, including Earth...
"I don't want to go..." the cry, little more than an agonised whimper, rippled through time and space. Drowned out by the song of the Universe, only the last remaining TARDIS heard the plea within those words and so she acted. Having been with this incarnation of her Time Lord far longer than any other, she could not bear for him to simply vanish, and so she did what was forbidden.
As his regeneration began, she took that which had made him who he was in this incarnation and hid it within herself. But the power was too great, even for the TARDIS and she knew she had to act before she and her Time Lord were destroyed.
Flames erupted from multiple panels as the power within her raged. Knowing she would soon lose everything, the TARDIS sacrificed her own chance at being reborn to save her most favoured incarnation.
As the windows of her shell broke apart and flames leapt into space, the TARDIS sent her innermost spark out into space, carrying with it the life force that had been the Tenth Doctor. As the regeration completed and her new Time Lord joined her, the TARDIS watched as the energy drifted towards Earth. She knew that when the spark landed, the residual regeneration energy would recreate her most beloved companion, allowing him to live on.
Little did she know what affect her actions would have on the very fabric of space and time...
