He couldn't help it. He just lied. He looked into her wide, curious eyes, and lied. About his planet, about his people. For the briefest of moments he could still see the red grass and expansive gardens about the academy, could still see the mighty citadel, and it had made him feel good.
But when he looked on the Face of Boe, he felt it in his hearts. They were gone.
And so was Jack.
So he fought to keep the wise, beautiful alien alive, to preserve the species.
And when the glass cracked, and the Face of Boe gave his last surge of energy, the Doctor had felt his hearts break. He looked on the last relic of an ancient race, and he wished in some small, desperate corner of his soul, that he was the one lying there.
Then the secret had come, and the Doctor shuddered. He knew he wasn't alone. And he knew he could never allow himself to fix the problem.
And when Martha asked again, this time about that mighty secret, he lied again.
He knew exactly what the Face of Boe was telling him.
Back in the TARDIS, hearts sore from telling part of the truth of the Time War to Martha in the rainy alleyway, he leaned over the console, the weight of Gallifrey on his back. With one quick twitch of the hand he could find the captain. After all, he was a beacon of light that the Doctor could see if he focused. The TARDIS herself would have no trouble. Jack was as soaked in artron energy as she was. Just a couple quick motions, a psychic affirmation to the TARDIS, and Jack would get a little surprise. Sure, he might rant and rave a little, but he'd get talked around...
No. He gritted his teeth, shook his head, and entered the coordinates for another jaunt into earth's past. He decided on an era that breathed Jack Harkness, the 1930's. He'd return to the London Blitz if Martha didn't accuse him of rebounding with her. It would be good just to lose himself in a memory for a short while. As he fought the urge to try and return to that last fractured piece of the Time War, he smiled at Martha, promising her another treat. After all, New New York had ended up with her stuck in a car, so it really couldn't be counted as a trip. At least, that was the lie he was telling them both.
Without her to stabilize him - and she was a very good anchor to keep him from going overboard - he had no idea what he might do.
And later, after the Daleks (again) and Lazarus, he tried to sleep and could only think of Jack. His hearts ached and he touched the cold sheets next to him and decided, if chance ever brought them together and the Doctor could run no more, he'd return the kiss.
