In series 3, ten and Martha are being chased by a species called The Family of Blood who want to use the Doctor's life essence to live forever. Because they can basically track him anywhere by the way time lord smells, he uses the chameleon arch to overwrite his DNA and make him completely human. The chameleon arch takes everything that makes him a time lord and puts it into a pocket watch, safe, until he opens the watch to become a time lord again. I don't know if I'm explaining that right, but it's close? The episodes are called Human Nature and Family of Blood and they are pretty good, if you ever get a chance to watch them (they'll probably be on BBCA on Wednesday when they marathon ten's episodes). Hope that helps!