The Daleks' death rays exploded all around as the Doctor leaped for cover. He found himself beside Romana, who said, "They're overwhelming us. We may have no choice soon." Romana had become president of Gallifrey since the Doctor had last seen her; she had also since regenerated again and her new self was a scrappy fighter quite comfortable leading the army of Time Lords from the front.
"I will not accept that yet," the Doctor replied. However, he also knew is options were limited. He was getting old, having gone through more than half of his regenerations. Indeed, Romana was shocked to learn that he had gone through four incarnations since they had last met. As such, he knew that this war could easily cause him to burn through his remaining selves and then, well, whatever came next. There was a way to stop it all, but it would mean taking down the other Time Lords along with the Daleks, and the Doctor was determined not to go that route unless there was no alternative.
Their enemies' cries of "EXTERMINATE!" grew steadily louder. The Doctor and Romana shared one last look, knowing that they would both likely have new faces the next time they saw each other. Both threw themselves into the fray as the Daleks burst through the room's defenses. The Doctor fired his weapon again and again, but it didn't seem to make any dent in the other side's numbers. Before long he felt a numbing pain all over his body, and knew that he had been hit. The Doctor fell to the ground desperately looking around for Romana, hoping she was faring better…
…………………………………………….
The Doctor awoke a few seconds later. He remembered what had happened, that he was now in his ninth form. His natural curiosity got the better of him at first; what did he look like now? But this thought was quickly shaken from him as he saw dozens of Daleks flooding the room. Terrified, the Doctor fled down a hallway, but everywhere he looked he only saw more. And soon, though he didn't understand how, he also began to see Cybermen, Autons, and all the other enemies he had faced over the years. None of them moved to attack him, but there was no time to question why. There was only one conclusion to make; the Time Lords were gone, he was the last one. And there was only one thing to do.
He ran left and right, remembering the complex directions to the last defense the Time Lords had built into their planet, to be used if it was ever overcome by enemy forces. He armed the device, then raced back outside, counting down the seconds he had to make it back to the TARDIS. It was tempting to seal his own fate as the same of the rest of his kind, but he realized that no matter what, the Time Lord race had to survive somehow.
He made it inside and quickly programmed it to leave Gallifrey, reappearing at a safe distance. Before leaving, the Doctor programmed the ship's cameras to keep showing him what was going on down on the surface; he wanted to see the destruction of those horrible beings once and for all. However, these thoughts turned to horror as suddenly the images of the Daleks and others changed to those of Time Lords. They were still fighting, Romana leading the charge. It hit him like a thunderbolt; his regeneration had gone wrong like it always did, and what he perceived as enemies had been his people all along. It had not been too late. But then…tears filled his eyes as he realized it was too late. The device he had activated could not be switched off. They were all doomed. A few seconds later a white light filled all the viewscreens as the Daleks and Time Lords alike were wiped from existence. The Doctor wandered around in a daze, unable to accept the finality of what he had done. Even worse, since it had been him that was responsible, there would be no way to prevent the event without causing a paradox. The Doctor was alone in the universe forever. As these thoughts slowly entered his mind, he found himself unable to move, and simply kneeled down and wept.