Rule of Two

""Always two, there are. No more. No less. A Master and an apprentice.""

- Master Yoda, Star Wars Episode I: The Phantom Menace

Sometimes the Big Bad gets bored doing everything himself. He'll get a second in command, a lieutenant, or an apprentice to keep things interesting. This is the Rule of Two. There are two big bosses, and both have to be taken down. If The Hero is about to take The Dragon down, expect the Big Bad to try to turn him to The Dark Side. If The Dragon is about to take the hero down, expect him to offer an alliance to overthrow the Big Bad and take his place.

Anime and Manga

 * In Naruto there's Kabuto and Orochimaru. And it should be noted that the Akatsuki only move in pairs.

Film

 * Star Wars is the Trope Namer. The Sith have the Rule of Two, where there can only be a Sith master training a student. The master cannot teach another student, and the student cannot learn from another Sith master.
 * In fact, there can be only two Sith Lords, the master and the apprentice, in total. The origins of this rule are explained in Darth Bane: The Path of Destruction, where the Sith have become so "corrupt" (from a perverse Dark Side point of view) that there are hordes of people with the title of "Dark Lord of the Sith", and their leader pretends to be just a first among equals; their official philosophy states that anyone claiming the title "Darth" or supreme leadership would only lead to strife an infighting. The Villain Protagonist Bane (who gradually becomes a peculiar variation of The Ubermensch) has been reading the ancient Sith texts and realises how against the traditional values such a policy is. Eventually, after, he comes to the conclusion that there should only ever be two Sith Lords at a time: one to hold power, and the other to covet it and take it by force when they're ready; and that the Sith should not work for the fall of the Jedi and to conquer the galaxy by armed conflict, but subtlety, which Palpatine eventually pulled off.
 * The actual Rule of Two itself is that each Sith Lord teaches one apprentice, and when that apprentice is strong enough, he (or she) will kill the master and take their place, choosing another student. In this manner, each master not only becomes strong, but must stay that way to stay alive, and each student must become stronger than their master. Each generation of Sith is stronger than the last, because any weak link in the chain is dead. A master cannot have more than one apprentice, because they will team up to kill the master while each of them is individually weaker than him, and will then turn on each other and weaken the Sith Order. In short, Chronic Backstabbing Disorder as a way of life and a code of morality.
 * When you think about it, a philosophy based on Hate isn't really conducive to long-term teamwork anyway...
 * It's not about teamwork, it's about power, and Obi-Wan finished the Sith's 10,000 years winning streak when he killed Darth Maul, also Palpatine was quite happy that Dooku was killed because he would soon get a "far younger and more powahful" apprentince.
 * The expanded universe makes it clear that pretty much every Sith lord and apprentice had extra force-sensitive people hanging around anyway, some of them on the hook with "okay so when I overthrow the master/my current apprentice has outlived his usefulness, then you'll be my official apprentice in our secret society."
 * Actually, although the Expanded Universe reveals that Palpatine, Dooku, Vader and other Sith Lords had their own minions trained in the dark side, the rule wasn't broken because they weren't true Sith Lords, but mere warriors or spies with some lightsaber training and little ability in the force.

Live-Action TV

 * In Heroes the Company's rule is "one of them, one of us"

Video Games

 * This is a recurring motif in Touhou.
 * Big Bad and her one-and-only dragon: Remillia-Sakuya, Yuyuko-Youmu, Yukari-Ran, Kaguya-Eirin, Eiki-Komachi (not bad folks), Kanako-Sanae, and so on.
 * Everyone have a counterpart (not necessarily yin-yang or dark side): Reimu vs Sanae, Chen vs Rin, Marisa vs Alice, Remillia vs Flandre, the list goes on and on...
 * Characters fight in pair during Imperishable Night.
 * Yukari Yakumo's ability is explicitly defined as the ability to manipulate border between two different things.
 * For that matter, the yin-yang features heavily in Touhou; it's even one of Reimu's attack mode.
 * Prominent in Fate/stay night. Sure, you could just kill the Master and run away from the Servant (it's even repeatedly stated to be the best strategy), but nobody ever does. Most apparent with Kotomine/Gilgamesh and Kuzuki/Caster. Nobody in either pairing is really the boss. Gilgamesh will do what Kotomine says, if he feels like it. Caster would obey Kuzuki's orders, but Kuzuki is too passive to really bother most of the time. Also apparent in Kotomine's fight against True Assassin and Zouken Matou.
 * In Batman: Arkham Asylum and Batman: Arkham City, the Joker keeps Harley as his right hand girl. Even if she's not very good at it.

Web Comics

 * In Evil Plan. Dr. Kinesis hires Alice as his second in command.

Western Animation

 * This is a common theme in Kim Possible. Drakken and Shego, the Seniors, and even Gemini says that he was saving the "Alpha" title for someone special.