I'm not actually a fan of Pertwee, but I agree he was very good here. The problem I have with this story is that it all seems a bit disjointed. Did the Master really have to go to all that trouble just to steal a missile? For that reason I couldn't give it full marks.
It is a bit of bizarre set up - I think that perhaps they relied on TV audiences being a bit naive and thinking that this was a big deal. It did seem a bit disjointed and perhaps that was because the writer, Don Houghton, was really a movie screenwriter and had a much bigger picture in mind when he wrote the script but then budget realities meant it was scaled back a little?