I've never quite known how to reconcile the video the Doctor left, or figure out when he recorded it, or why, instead of just telling Martha what was going to happen. But my best guess is that he knew the Family was after him before the scene that we got—the one ending with "Oh yeah, it hurts" and then him with the Chameleon Arch on his head—and made it then, just in case he got desperate enough to decide to go with the plan he eventually did.
Comments on my characterization are appreciated. But also know that I wrote this thing some time ago. Oh, and I don't own Doctor Who, nor is this fic making me any richer.
"Oh yeah," he said certainly, and looked over at her, appearing oddly unconcerned. "It hurts."
Martha stood still, trying to take it all in as he continued to adjust and readjust the controls. After several seconds the Doctor glanced over at her again. She must have looked more afraid than she thought, because he stopped and seemed to soften a bit. "If it's any consolation," he offered, "I won't remember the pain."
"What will you remember?" she asked sadly.
He looked slightly alarmed, as if he hadn't anticipated the question. "Well… When I say 'remember'… it's not that I won't recall things so much as I'll just be a completely different person, and the 'me' that you know will be inside that watch." He pointed to said watch, and Martha looked down at it. It looked totally ordinary.
She held it up between her fingers. "You're gonna be inside this thing?"
He offered a small smile, but it wasn't a happy one. "Basically."
After a moment, she circled back to her question. "So you won't remember this?" She waved her hand in a gesture meant to take in the situation they were currently in. "Any of it?"
"You, me, the TARDIS, the Time Lords. Gallifrey. All if it. Gone." He stopped and suddenly closed his eyes, clearly pained by what he was saying. Martha would have hugged him if she hadn't known how much he loathed showing vulnerability. A hug would not help. After a moment his eyes flew open and he continued, "Everything I know now will be gone, replaced by a false human memory."
She felt tears suddenly stinging her eyes at the thought of losing him. "Isn't there anything else you could do?"
"Three months," he said, placing his hands on her shoulders in a gesture that said Be strong. "The Family can last only three months. Then they die. Like mayflies. Unless they find me, which is what we're trying to avoid. What we will avoid. We'll let them waste their short lives looking for the wrong form of me and then we can go back to life as it should be. Traveling around and finding trouble to run from on our own. We don't need this extra help, right?"
Finally, she smiled. Just a little, but there it was. "Promise?"
"Cross my hearts," he said, holding a hand up. "Scout's honour." Martha watched as he continued to fiddle with the device, calibrating it and recalibrating it until it could suit his needs to the utmost. After a few more moments of this he paused, looked at the controls, nodded decisively, and turned to face her. "There's a video, stored in the central console. Instructions to open it are in the manual—you know where to find that, if you need it. It's titled 'For Martha.'"
She nodded, and said, going for a lighthearted tone, "Easy enough to remember."
The Doctor didn't smile, though she didn't blame him. He positioned himself underneath the Chameleon Arch, and strapped it onto his head—only to pause, and look over to her, meeting her eyes one more time. "We'll be on Earth. That's a given. But anytime, anywhere. Be ready for anything."
She clutched the fob watch like a lifeline. "I'll miss you."
His eyes looked so sad. But he gave one last small smile. She knew he couldn't return the words. He wouldn't be able to miss any of this. He wouldn't know.
The Doctor switched on the Chameleon Arch, and lost himself in the watch in Martha's hand.