New chapter, as promised.
Acceptance
"Doctor?" Martha took a step towards the new man. He looked at her.
"Yes Martha. It's me," he confirmed. Martha swallowed hard.
"Wow," she breathed.
"Are you alright?" asked the man who Martha now knew to be the Doctor. "I understand if you're shocked. Some people find it hard to adjust – myself included, if I'm honest."
"It's okay," said Martha. "You're an alien. You ... change bodies..."
"It's called regeneration," said the Doctor.
"You mean like in plants?" questioned Martha. "I know in some places after fires, the plants renew themselves, though they don't end up becoming completely different plants..."
"Martha, slow down," said the Doctor, approaching her. "You've got the right idea, but that's not the point. You always try to act so objectively around me."
"Well what else am I supposed to do?" asked Martha. "The Doctor I knew exploded into light and morphed into another bloke. After what I've seen, I don't see why I shouldn't be able to accept that." The Doctor grinned.
"Brilliant!" he said. "So, what do I look like?" Martha blushed.
"Well..." she began, but before she could continue the Doctor lurched over in pain. The TARDIS seemed to share his agony, as it was violently rocking from side to side.
"The regeneration is going wrong," gasped the Doctor. "I can't stand the pain. Oh my head..." The Doctor held onto the central console and managed to program new coordinates in.
"Where are we going?!" cried Martha.
"Back to London," said the Doctor. "I'm going to need all the help I can get..." The Doctor cried out, and he and Martha held on tight as the TARDIS took them to London on Christmas Eve.
You might notice a few hints of the second chapter in here. That's just how I see Martha.