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.
It's usually understood that the two want to keep it that way. Never introduce a third, and quickly replace the other if they go down. Due to infighting or general For the Evulz culture, the Big Bad may decide to dispose of the Dragon himself and get a new one. Similarly The Dragon will overthrow the Big Bad if the opportunity presents itself, and bring on a new Dragon of his own. The tension of this dynamic is that they rely on each other, but both know it's a race to see who will stab who in the back first.
The Hero is usually the prime candidate for the replacement. 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. Compare and contrast Big Bad Duumvirate, Deceptive Disciple and Bastard Understudy. Not related to Rule of Three.
- In Naruto there's Kabuto and Orochimaru. Then there were Zabuza and Haku.
- Madara and Obito, started like this but Madara died shortly thereafter leaving all the work on Obito and when Madara revived, they became Big Bad Duumvirate.
- Kaguya and Black Zetsu. Although the dynamic isn't really there since Black Zetsu is the one calling the shots, as Kaguya has absolutely no personality at all.
- Crouching Tiger, Hidden Dragon: The apprentice (Jen) is a more skilled combatant than the Master (Jade Fox), but the Master is more treacherous.
- Star Wars is the Trope Namer. The Sith have the Rule of Two, where there can only be a Sith master and an apprentice - no more, no less one to possess power and the other to desire it. The idea is that each Sith Lord teaches one apprentice until they are strong enough to destroy the master and take their place, at which point the apprentice will take on a student of his own, or until the master kills the apprentice and gets a new one. 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 may team up to kill their master despite being individually weaker than he or she, 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.
- The origins of this rule are first explained in the Revenge of the Sith novelization, and explored further in Darth Bane. When the Sith order was originally created, it was indeed an order that had many members, but since they were all steeped in the dark side, they had a collective bad case of Chronic Backstabbing Disorder. This tendency to betray each other at the drop of a hat weakened the order to the point where the Jedi (who as light-siders were more unified) were gaining the upper hand. To combat this, Bane decided that there should only be two Sith Lords at one time- a master to have power and an apprentice to covet it. He also decided that they should endeavor to take over the galaxy via subtlety and manipulation (like Palpatine eventually did) instead of outright invasion. Having made up his mind on this, he manipulates all collectivist Sith Lords into committing mass suicide.
- Interestingly, 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 technically broken because they weren't "true" Sith Lords, but mere warriors or spies with some lightsaber training and ability in the force. However, it seems that once a minion begins to grow too strong, or worse is discovered being trained in the Sith arts, one of them has to die, be it minion or master. Or potentially the apprentice, with the minion becoming the new apprentice.
- Darth Tenebrous broke the rule by recruiting two apprentices and not telling them about each other. After Darth Plagueis "took over", he was surprised by Darth Venamis, who had learned of him, was better at the use of the lightsaber and had been trained in Plagueis' style. Plagueis was smarter, imprisoning Venamis and experimenting on him for years. Venamis compounded the issue by having several potential apprentices lined up himself, even before he had dealt with Tenebrous and Plagueis.
- After claiming the mantle of Sith Lord from Tenebrous, Plagueis did away with the Rule of Two entirely, seeing no point in raising a successor when his experiments into immortality meant he would live forever. He recanted this to an extent when he met Palpatine and was so impressed with the young man's potential he felt compelled to train him. In his reckoning, though they were two Sith and had no intention of training any others, because the two were going to rule as equal partners (once Palpatine was fully trained) there was no need for a fight for dominance. That said, given he acted like Palpatine's superior even long after his apprentice had become quite powerful, it's clear this was something of a rationalization for him. Palpatine certainly thought so and while killing Plagueis lectured him on the arrogance he had to assume he would be somehow exempt from the constant Sith struggle for power.
- Palpatine deceived Plagueis into thinking that Darth Maul was simply an assassin, not a true apprentice. The one thing that didn't go according to plan was that Maul was defeated right after Palpatine disposed of his own master...though Palpatine made that work to his advantage by accelerating the training of Dooku, who was better suited than Maul had been for the very public role needed in the next phase of the plan. Of course, Palpatine was mentoring Dooku while Maul was still his apprentice, making Palpatine a rather blatant Hypocrite.
- Conversely, Palpatine began to suspect that Dooku was plotting the same in Star Wars: The Clone Wars with his own assassin, Asajj Ventress, and ordered him to have her killed to prove his loyalty. Dooku followed through with the order but failed to have her killed, resulting in her turning on him.
- After said betrayal, Ventress herself recruited her own apprentice in the form of Savage Opress with the intent of taking revenge on Dooku after her attempt to do so herself failed, but with the aid of Mother Talzin sent him to Dooku under the guise of "training" as a new apprentice due to exploiting the paranoia he built up after the failed assassination attempt. In the end, however, Savage betrayed both of them after he got sick of their abuse and ran off to find his still-alive-but-not-quite-sane brother Maul with the aid of Mother Talzin, whom he became the true apprentice of. As can be plainly seen, the Rule of Two at times was more a guideline than a rule.
- When Palpatine confronts Maul and Savage on Mandalore, he chastises Maul for breaking the Rule of Two. He conveniently omits that he was training Dooku while Maul was still his apprentice, making Palpatine a Hypocrite of the highest order.
- Since Star Wars Rebels has canonized the Imperial Inquisition, they are Dark Side Force-sensitives employed by Darth Vader, but are immune to the Rule of Two because they are not Sith. They're purposely trained so as not to reach the Siths' power level as they would run the risk of violating the rule like Asajj Ventress did.note
- It's revealed in the season 2 finale that despite having immense rage at the Sith Order as a whole for betraying and discarding him, Maul still adheres to this philosophy. And he's looking to corrupt Ezra into becoming his apprentice.
- Ultimately Darth Bane's philosophy, while it kept the Sith alive in secret for millennia, also resulted in the order's undoing, as the chain could be easily broken by a factor that Bane failed to take into account-the potential redemption of either the master or the apprentice. Darth Vader's Redemption Equals Death and, in the old Extended Universe, Jacen Solo/Darth Caedus' apprentice renouncing the Dark Side of the Force and the Sith shortly after the former's demise, pretty much spells the end for the Sith Order because of the Rule of Two. What's worse is that Bane really should have known better. The Sith Lord whose Holocron gave Bane the inspiration for the Rule of Two, Darth Revan, had also renounced the Dark Side, and Bane knew this.
- The Last Jedi exposes another flaw in the Rule of Two related to the redemption example above - a Sith apprentice killing his master but deciding to destroy the entire Sith doctrine out of some sort of principle. While Snoke was not a Sith lord, Kylo Ren still betrayed him, and comes to the realization that both Jedi and Sith doctrines are intrinsically flawed, and that the past should be let go of... By being destroyed completely.
- 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.
- 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. He's stronger than Assassin, but can't kill him due to him being a Servant, so he has to take out Zouken first and then Assassin would be vulnerable. But Zouken is essentially unkillable by normal means plus Assassin is keeping him busy.
- Magical Battle Arena has Ruru Gerard and Nowel Diastasis as the two primary antagonists of the game. This is however dropped in the sequel which sees Ruru Put on a Bus.
- The two major villains of Mario & Luigi: Superstar Saga are Big Bad Cackletta and The Dragon Fawful. In Bowser's Inside Story, where Fawful is the Big Bad, he gets a Dragon of his own, Midbus.
- 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. As for what that means in practice, it apparently means whatever Yukari wants it to mean.
- For that matter, the yin-yang features heavily in Touhou; it's even one of Reimu's attack mode.
- In Evil Plan. Dr. Kinesis hires Alice as his second in command because he loses his previous number two.
- 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.