Music for the Article
A Genre Savvy character doesn't necessarily know they're in a story, but they do know of stories like their own and what worked in them and what didn't. More sophisicated versions will also know they can't tell which genre they are in (and are often in far more realistic or complicated genres that the stories they remember), or which characters they are.
Some villains don't play by the rules. A point comes when a typical Bond Villain would make the tiny, critical but common mistake that would lead to their defeat like every other villain before them in an identical situation.
He will captures the heroes in an indestructible cage, rigs the cage to be flooded, and throws away the key, which gets eaten by one of many giant crocodiles in the area. For bonus points, the key thrown away was a fake, and the real one was with the Villian the entire time. He also anticipates every possible counter to his plans, including taking into account Heroic Battles and such.
The amazing thing about this plan is it actually had no mistakes in it. The only reason the Heroes get out of this is because The Villian didn't know that there was another member of the group, who would come and break them out of the cell. If The Villian had known that he existed, they would have been doomed. Not only that, he has three layers of plan to defeat the Hero. The only reason he fails is because of a massive amount of the Heroes power.
He fires at innocent bystanders during his epic fight with the Big Good to make his opponent weaken himself to protect them, backstabs, and eats the partner he was allied with before he outlived being useful stage, attacks one of the Heroes in the middle of a long Transformation Sequence, and finally defeats The Heroes superpower by actually taking the time to analyse it instead of just wasting his time screaming "This Cannot Be!", He was very close to actually winning....but was overwhelmed
They Porcceded to manipulate the heroes (who were, at that time, more powerful than them) using the body of a little girl (knowing they wouldn't hurt them while using that body), convincing the good guys to attack their opposing organization and hunt some people (some which were good) after giving them the Upgrade they were searching (knowing that they will get a better deal in the end) and almost destroyed the main characters with success after achieving their goals: In the end, the good guys defeated their biggest foe for them, they got a new body (and got even more powerful), and didn't lost anything for that.
The only part that didn't work was trying to destroy the Hero. the Villian apparently didn't consider Mr. Big Good sending very high members along too. Not that this caused much of an issue for the Villian, they adapted before and did so here, retreating rather than getting into a fight they couldn't be certain of winning.