Wasn't the real reason the Doctor asked her to come with him because he'd realised something was going on?
By the way, regarding that Law And Order crossover. Theta Sigma was the Doctor's nickname at college. That fic says it's his real name. It's not.

Hehe This is the episode that introduced them all! I saw this before any of the others and number 11 hooked me :D I like the thought of looking into his thought process... is that creepy?

Very nice.

You got his thoughts spot on, as in-Character as you can get him after just one episode with him