To Catch Heroes, Hire Villains

So, things are looking pretty grim. The Hero has just been shown to be guilty of a crime (how serious doesn't really matter), and now they're on the run. What's a Lawful Good aligned police commissioner supposed to do? Clearly, there's only way to deal with this problem. Hire the biggest, baddest, most evil character you can find and make them hunt those dirty heroes down, just like they try and fail to on their own every week.

...Well, maybe not the best logic around, but what do you expect? We're talking about tropes here.

The idea here is pretty simple. You want to show the conflict the heroes have with the people they're trying to protect, but if they go up against cops, they have to ponder weighty questions like, "Should I really be attacking police officers who are only doing their job?" And that's no fun at all, since a lot of shows are looking for action as opposed to Angst. So instead, hire a villain to take them down. That way, when the huge action scene comes around, we don't get disappointed. The chances, by the way, of the whole thing being a huge frame-up designed to make the heroes look bad are reasonably high.

Anime

 * In Outlaw Star, after Hilda steals Melfina and the titular starship from the Kei Pirates, they manage to track her down with help from the MacDougal brothers. A little more ambiguous than hero/villain since both Hilda and the MacDougals live outside the law, but they're certainly more heartless and ruthless than she is, and go on to be one of Gene's worst enemies.

Comics

 * Civil War features Tony Stark hiring legions of supervillains to capture the resisting supers. Thunderbolts is an interesting example because the villains are the protagonists.
 * And of course it blew up in his face; Norman Osborn is the director of SHIELD HAMMER.
 * The original Freedom Force in the Marvel Universe: The Brotherhood of Evil Mutants agreed to serve the U.S. government in exchange for full pardons for their past crimes. Their second mission was to bring in the Avengers, who had been framed by Quicksilver.
 * Averted in The Dark Knight Returns, where the cops face Batman themselves, and get their ribs broken.
 * In Superman/Batman: Public Enemies, President Luthor frames Superman for endangering the Earth and forms a posse of superheroes led by Captain Atom to bring him in--plus he puts Major Force on the team, one of the most sadistic villains around (the phrase "Women in Refrigerators" refers to a murder he committed. He's pretty vile.)
 * Early Spider-Man comics had J. Jonah Jameson hire villains, or in case of the Scorpion help create him in order to try and take down Spider-Man.

Video Games

 * In Tin Star for the Super NES, the townspeople elect Black Bart, the game's villain in every previous "day" of gameplay, as sheriff after Tin Star is framed for the murder of a small child. He isn't actually dead.
 * In City of Heroes, one Story Arc has your character become a fugitive (although it doesn't really affect jack, of course). You get ambushed a couple times by Malta and once by a Nemesis group, the former suggested to have actually been hired by the city.

Live Action TV

 * Not an exact example, but in the Doctor Who episode The Five Doctors, the Time Lords recruit The Master to save the Doctor, who is trapped in the Death Zone on Gallifrey.

Western Animation

 * Avatar: The Last Airbender: After Toph Bei Fong commits the crime of leaving the her family's Big Fancy House to help the Avatar save the world running away from her family at the age of 12 without telling them where she's going, Toph's dad hires the thug which Aang and co had just spent the half the episode fighting (mainly because he managed the feat of successfully kidnapping Toph and Aang earlier) to track Toph down. It actually works, until Toph manifests an ability that nobody else in written history has ever done and everyone thinks is completely impossible.
 * When Aang disappears near the end of the third season, the rest of the group turn to their newly acquired Lancer to find him. When he asks why, they point out that before his Heel Face Turn, he had spent two seasons tracking the Avatar down over and over again, and as such is the most qualified one to do it now.
 * In one episode of Batman: The Animated Series, after Batgirl dies (All Just a Dream), Gordon releases Bane to bring in Batman.
 * In Justice League Unlimited, Project Cadmus is a government organisation aimed at creating pre-emptive measures should the Justice League go rogue. It is largely composed of supervillans and is funded by Lex Luthor.