The clone was not happy. Just as he was getting settled into life with Rose on Pete's World, a newly resurrected Master showed up and kidnapped him.
Bad enough that the Master was back, it also turned out that he had grown his own TARDIS and was planning to conquer the universe (again!).
To make matters even worse, instead of being subjected to the usual torture, the Master merely smiled wickedly and said that he, the Master, out of the goodness of his hearts, was going to restore him to a proper Time Lord body. Not surprisingly, the clone didn't find the Master's words to be particularly reassuring.
Resigning himself to his fate, the clone stopped trying to fight the anesthetic the Master had administered and surrendered to unconsciousness. His last thought was that perhaps, at last, he'd be ginger.
Some time later:
The clone awoke, felt two hearts beating in his chest and felt a rush of relief. The Master actually kept his word, the clone thought in astonishment. I'm in one piece and I'm a real Time Lord again. Rassilon, now I'll have to be grateful to him, he thought.
The clone decided to take stock of his new body, starting with the top. Ginger hair, rather long ginger hair at that, the clone thought, rather pleased and surprised at the Master's thoughtfulness. Rather small hands, though, and for some reason, he couldn't see his feet. It took a moment to register that his view was blocked. The clone tried to smooth down the two lumps blocking his view for several minutes before coming to the horrified realization that they were attached to his chest.
Realization dawned. The door opened and the Master returned. "Wake up sleeping beauty," he said, smirking. "I said I'd give you a Time Lord body, I didn't say it would be male, now did I?" The Master turned on the sound system, filling the room with the sounds of Barry White, poured two glasses of champagne and said, "now, about recreating the Time Lord race, no time like the present,"
The clone fainted.