48. Enlightenment (Fifth Doctor)
The conclusion of The Black Guardian Trilogy, which had its ups and downs. It featured the Black Guardian essentially hiring someone to get into the Doctor's entourage and look for an opportunity to kill him. In this story, the summation of that arc, the TARDIS lands on what seems to be an Earth sailing vessel, but the crew - while content there - do not seem to remember how they got there, how long they'd been there, or even where they were going. Eventually it's revealed that they're in fact flying through space on a ship commanded by an immortal alien. Not only that, there are many more of these aliens with their own ships, and they're racing in a dangerous course. The prize for winning the race: Enlightenment.
47. Mark Of The Rani (Sixth Doctor)
For 14 years, The Master had been one of the Doctor's most feared and capable enemies. So when it came time for the sixth Doctor to face him, they kicked things up a notch (BAM!) by adding another renegade Time Lord to the mix, The Rani. She was unique from the Master by being not an ego-tripping power-mad villain, but rather just being a horribly unpleasant person. She's a genius scientist and views everything as secondary to her research, caring not for ethics or peace. This story features her and the Master teaming up against the Doctor, seeing him as the only person standing in the way of their respective plans. The serial takes place on Earth in the 19th century, during the height of the Luddite rebellions against machinery and technology, which makes for an intriguing backdrop.