Emergency Protocol One
He waited until he was sure she was asleep. The Doctor had never done this before—before the Time War he was too young and brash to imagine the consequences of failure. He pressed a few buttons on the console and began speaking.
"This is Emergency Program 1. Rose, now listen, this is important. If this message has activated, then it can only mean one thing: we must be in danger, and I mean fatal." She was in danger every moment she spent with him, after all.
"I'm dead, or about to die any second with no chance of escape. And that's okay, I hope it's a good death." Life was such a fragile thing, even for Time Lords. Any foe that required this activation would be capable of killing him permanently. And if he somehow survived—memories of the trauma surrounding his sixth regeneration hardened his resolve. He couldn't risk that happening again.
"But I promised to look after you, and that's what I'm doing. The TARDIS is taking you home." She wouldn't take that easily—he knew that already. Might as well address that in advance. "And I bet you're fussing and moaning now. Typical. But hold on and just listen a bit more. The TARDIS can never return for me. Emergency Program 1 means I'm facing an enemy that should never get their hands on this machine. So this is what you should do. Let the TARDIS die. Just let this old box gather dust."
Through his mental link, he could feel it shudder. Do you want to explore time and space piloted by a lot of stupid apes? he asked it before continuing. "No one can open it, no one will even notice it. Let it become a strange little thing standing on a street corner. And over the years the world will move on, and the box will be buried."
Maybe she'd never see this. Maybe she'd just leave someday. They all did, eventually. But if it was ever activated— "And if you want to remember me, you can do one thing. That's all, one thing." He breathed into the TARDIS, releasing a physic echo; just enough of his life to give a real goodbye. "Have a good life. Do that for me Rose. Have a fantastic life."