To be slightly more precise, in the TARDIS console room was a young bloke wearing a towel and with a toothbrush in his mouth and a perplexed look on his face.
"Amy?" the puzzled boy asked, recognizing her. "What's going on here?"
Amy's bright red hair swept around her face as she swiftly turned to the Doctor. He was just as confused as she was; only he had much more experience with hiding it.
"That… is not good." He threw a glance at the screens and read the problem in the many circles and figures.
"What happened?" Amy asked.
"Well, we landed on top of him. In his bedroom, so the TARDIS performed the safety protocols; she placed the individual that might be harmed in the safety of the console room."
"So we just picked him up out of his bedroom."
"Apparently, yes. " he told her with a concerned look in his face. "That doesn't always happen. I must have forgotten to tell her to avoid people."
"Excuse me!" shouted the little man. "Can someone explain to me what is going on?"
The two time travellers both turned and looked at him, like they had forgotten for a moment that he must have been terribly confused. The Doctor's face brightened up as he recognized the face.
"Jeff!" he greeted, jumping over the stairs and kissing both his cheeks. "The boy who saved the world that one time, wasn't it? Look, Amy, it's Jeff!"
He turned to look at Amy and almost expected a similar reaction.
Amy just walked very slowly towards him. She had a look of suspicion.
"You wearing any pants?" she asked cautiously
"No."
He stared fiercely at her for a moment, as if trying to telepathically tell her that he needed both clothes and a serious explanation.
"Don't worry," she ensured him. "We'll get you back in a moment."
"Or..." the Doctor said holding up a finger in the air as if raising his hand with a suggestion in class. "We don't."
"We don't?"
"Yes."
"Oh." She got it not. "We could do that."
"We really could."
"Excuse me!" Jeff shouted again, trying to look slightly more worthy of respect, even though he was wearing a towel. The Doctor turned to him with a smile.
"Jeff, how would you like to join us for a trip in my time machine?"