The Good, the Bad, and The Evil

So Draco in Leather Pants and Anti-Villain baddies are making your villainous faction more popular than your protagonists. However, they're really good villains too, and you don't want to get rid of those. So what's a writer to do?

A faction split, of course. Arms will be taken up, Anti Villains will fight Complete Monsters, Enemy Civil War erupts, and the end result will, at the least, be a Melee a Trois, but more likely, this slides into Enemy Mine by allowing the Good Antagonists to join with the actual protagonists, as a way of sidestepping that pesky Failure Is the Only Option rule that most bad guys inevitably seem to be stuck with.

A subtype of Enemy Civil War in that the splinter factions tend to distinctly divide between "Actual Bad Guys" and "People the Good Guys Can Work With". One faction may claim that they're Eviler Than Thou, the other faction may respond that Even Evil Has Standards and anyway they are A Lighter Shade of Grey.

Compare Morality Kitchen Sink, in which characters from everywhere on the moral spectrum are present but they aren't conveniently sorted into white, gray, and black factions.

Anime and Manga

 * Mobile Suit Gundam SEED had this with the Three Ships Alliance, which notably took the more morally upright members of the Earth Forces and ZAFT and put them into a faction that was (mostly) dedicated to Doing The Right Thing instead of racist genocide. Subverted in that certain members still stayed with either faction for better (Yzak) or worse (Natarle).
 * Continued in Gundam Seed Destiny, with the Three Ship Alliance which had most of the previous members in it, the supposedly Well Intentioned ZAFT forces under Durandal, and the Blue Cosmos/LOGOS forces who are pretty much evil.
 * During Fullmetal Alchemist, Yoki, Scar, Barry the Chopper, Greed, and Kimbley's chimera are all introduced as antagonists to the Elric brothers. However, all end up joining the heroes at various points to fight against the main villains, Father and the other homunculi.
 * Greed worked for Father, too; they just had their family strife civil war before the plot began. Or the main characters were even born. It was a pretty tightly plotted series.
 * Hellsing has the Hellsing Organization (mostly good), the Iscariots (bad), and Millennium (evil). At the end of the series the Iscariots briefly team up with leave Hellsing alone to fight Millennium.
 * The exact words of the trope were used by Cartoon Network to advertise Dragonball Z at one point, referring to Goku, Vegeta and Freeza respectively.
 * Saint Seiya: The Lost Canvas; Athena's army is the good,.
 * In Saint Beast, the Saint Beasts are the good, Lucifer is the bad, and Zeus is the evil, although initally the latter two seem the other way around. The angels know things aren't right with the missions Zeus is sending them on but reject Lucifer's offer to join him because they know he's responsible for demons attacking humans. However, when they finally decide to rebel against Zeus they end up on the same side as Lucifer without actually agreeing to work together.

Comic Books

 * In Star Wars Legacy, it is finally estabilished for good in Star Wars canon. The Empire is split into Darth Krayt's Sith Empire (the evil) and Roan Fel's Empire (dictatorial but not really evil).
 * In G.I. Joe, this eventually happened in Cobra's ranks. Serpentor's splinter group the Coil fought against Cobra proper. Of course, matters only become more complicated when you realize that Cobra was already a little shaky, being an alliance between Cobra Commander's actual Cobra forces, Destro and his Iron Grenadiers, Zartan and the Dreadnoks, Tomax and Xamot and the Crimson Guard, independant contractors like Dr. Venom, Kwinn, Major Bludd, and Blackout, and Firefly and the Arashikage ninjas, with each group constantly vying for ultimate supremacy... Cobra's got to be one of the least stable factions in all of fiction, really.

Fan Fiction

 * The Open Door has developed into a situation like this with dozens of sides in all three corners. Most notably, the main characters may be the Bad or the Evil depending on your opinion of them (They definitely aren't the Good, not with Nanoha and the crew around to be compared against them).

Films -- Live-Action

 * The film Hard Rain does this with its three main characters. Tom (Christian Slater)'s security guard is the good, with Jim's (Morgan Freeman) armed robber apparently the bad, as his gang attempts to rob Tom's armoured car, and were responsible for killing Tom's uncle Charlie (Ed Asner). In a twist, the Evil is the corrupt Sheriff who likewise goes after the money from the truck, which Tom had hidden. When Jim is revealed to have been in cahoots with Charlie and had not wanted to kill anyone, he teams up with Tom, kills the Sheriff and Tom lets him escape.

Literature

 * Honor Harrington does this with the second coup d'etat of Haven, firmly putting the Anti Villain group in control of the government, and a lot of the former SS and power hungry types out on the run as renegades. Notable for having it simply flip the status quo in a few areas: there're still bad Havenites, but now they're the exception rather than the rule
 * After the Emperor's death, the Empire in the Star Wars Expanded Universe started breaking up. Various captains and admirals left with their forces and became warlords, sometimes rejoining the Empire later, sometimes the New Republic, sometimes becoming isolationist, and most often fighting everyone. The Courtship of Princess Leia and three books of the X Wing Series deal with the New Republic's campaign against Warlord Zsinj. In Courtship he's a cardboard baddie, but in the X Wing Series he's really clever and nasty. Enough so that both the Empire and the New Republic form task forces to take him down, and surreptitiously they end up working together, both aware that this wouldn't last and if this cooperation was ever reported they'd face treason charges.
 * Warlordism and the attrition that comes of a new leader rising to the fore, striking the New Republic, and getting beat down eventually whittled the Empire down small enough that Captain Pellaeon, who'd patiently served under each leader and picked up the pieces after, was forced to join a warlord. Eventually, during the Jedi Academy Trilogy, Daala talked the various warlords into meeting together to try and get them to join forces; she and Pellaeon sat out their arguing, then put on gas masks and watched the warlords die. Then Daala lost a good portion of this newly-replenished Empire and left it to Pellaeon. A few years later, and Supreme Commander Pellaeon worked to make peace with the New Republic, while other elements of the Imperial Remnant fought furiously to prevent this. Decades after that, Grand Admiral Pellaeon was one of the heroes' most reliable allies.
 * In The Dresden Files, Johnny Marcone turned out to be such an intensely awesome Anti-Villain that he's on Harry's side more often than not. This irritates Harry, who really, really wants to be able to write him off as "criminal scum," but has some trouble with that when Marcone is going to incredible lengths
 * In Mistborn you have several levels of this- Vin, Elend, and Sazed are the good, Kelsier and most of the skaa rebellion are pretty good, the Lord Ruler and most of the human bad guys are the bad, and.
 * Do note, though, that Vin is the one who states something along the lines of "Good? Bad? I'm just here to kill people."
 * At one point in his commentary, Sanderson points out that a particular fight is "a good, old-fashioned showdown between good and evil! Or, at least, between Kelsier and evil".
 * In the Darkest Hour, Thunderclan and Windclan, the two heroic clans, team up with Shadowclan and Riverclan, the two villainous clans, to fight a worse evil; the Complete Monster Scourge, who wants to take over their territory.

Live-Action TV

 * During season 4 of Lost, Ben, Affably Evil and Magnificent Bastard that he is, talks his way into sort of teaming up with the good guys against Psycho for Hire Keamy and his men, although Ben still had his own agenda the whole time. Keamy becoming more expendable than Ben after he proves that he is a Complete Monster by, and is eventually killed by Ben himself.
 * The season 2 finale of Buffy the Vampire Slayer ends with Buffy teaming up with Spike to stop Angelus from destroying the world. As Spike explained it, he likes the world; lots of fun things to do and plenty of humans to eat. Although Spike decided "screw it" halfway through their team-up and left with Drusilla.
 * I think that was the original plan—he got her in and took out half the threat, then left her to risk her life on her own. May be considered the first instance of his having faith in her? More to the point, he likes the world to live in. If he gets killed trying to save it, no point to the saving.
 * To say Dollhouse uses this trope a lot would be to understate dreadfully. While actives themselves are good, Paul Ballard is good-ish, and the entire LA Dollhouse staff is deeply grey. We all just agree Alpha is evil as are the people in charge of Rossum as a whole.
 * And by the end this has fragmented even further.
 * Sons of Anarchy takes this and shifts it a few steps down the morality scale. The Sons are at best a Villain Protagonist group and tend to team up with some very nasty people to take on enemies who are even nastier characters.
 * The IRA are a long time ally and business partner of the Sons but lately Jimmy O'Fallon is trying to cut the Sons out of the lucrative gun running business. However, he has a lot of enemies among the other leaders of the IRA and they try to use the Sons as a weapon against Jimmy. So while Jimmy is the evil guy, it is a toss up whether the Sons or the IRA are the 'good guys' in this mess.
 * Well, Hale could have been considered the "Good" . And really only Clay and Gemma can be considered Villain Protagonists, the others are more Type 5 Anti Heroes with Jax and Opie straddling the line between types V and IV.
 * The Cape (trope) now seems to have established something like this with the Cape as the Good, the Carnival of Crime as the Bad and Fleming/Chess as the Evil. it may even be a fourway with Scales somewhere between the Carnival and Fleming.
 * Juken Sentai Gekiranger, sort of. GekiJyuKen school is the Good, RinJyuKen school is the Bad, where GenJyuKen is the Evil.
 * Season 2 of Nikita is shaping up like this, with Nikita and her allies as the Good, Division and their Man Behind the Man Oversight as the Bad, and Gogol and their Man Behind the Man Zetrov as the Evil.
 * Though it should be noted that Division only seems better than Gogol and Zetrov because Alex is in an Enemy Mine against the latter two with the former. And on top of that, somewhere between Bad and Evil we have Amanda (who runs Division but is now plotting against Oversight) and Percy (who's plotting against everyone).
 * Following the status quo changing events about midway through the season, the list is a bit different now—Team Nikita is still the Good, but Zetrov's head Semak is now closer to the Bad, and the Evil can be best represented by Amanda  , with Percy still somewhere between Bad and Evil.

Videogames

 * In the Halo series, an Enemy Civil War divides the Covenant between the Elites and the Brutes. The Elites join forces with the humans and eventually make peace with humanity when the war ends.
 * Mass Effect 2 has Paragon Shepard, his/her crew, and Anderson as the only spots of good, the politicians and people like Aria in the grey area, and various mercenary groups, the Collectors, and the Reapers as evil.
 * In the Dune II, Dune 2000 and Emperor: Battle For Dune games you have 3 playable factions (minus the subfactions, you can be allied to those) that fit this trope, the good House Atreides, the insidious House Ordos that is willing to do nasty things if necessary for it's endless pursuit of wealth and probably drugs its citizens to make them more submissive, vs. the evil House Harkonnen who are a royal house consisting almost entirely of perverted, deranged psychopaths who enslave, backstab, and a lot of other nasty things and their soldiers are more afraid of them than their enemy.
 * In the Free Space stategy guide, it describes the Terrans as the "Good Guys," the Vasudans are the "Bad Guys," and the Shivans are the "Really Bad Guys."
 * Mega Man Zero: Zero, Ciel, and La Résistance are the Good; Copy-X, the Guardians, and Neo Arcadia in general (or rather what Neo Arcadia has become) are the Bad; and Dr. Weil and Omega are the Evil.
 * Elpizo
 * Something like this happens in Fallout 3 with the Enclave splitting up. An interesting variation as the player is actually given the option of siding with the more evil faction.
 * Command & Conquer, starting with Yuri in Red Alert 2, the Scrin faction in Tiberium Wars (double the fact that the Brotherhood of Nod has received even more fandom by this time). Not so much in Red Alert 3, since the 'bad guys' are technically still the Soviets.
 * Blaz Blue also adheres this, although there's no pure Good or Bad due to the rather gray moralities of both sides. Oppositions of the NOL (Ragna, Sector Seven) is the Good. NOL is the Bad. Hazama/Terumi and Relius Clover are the Evil.
 * Psychic Force, by the second game, exemplifies this. The Good is Anti-NOA (no official leader, the closest is Burn), the Bad is NOA (led by Keith), and the Evil is the Army (led by Wong). There are other forces such as magicians (Genma/Genshin) that don't take sides and instead be a Knight Templar and just target all three sides because they're Psychiccers and Psychiccers are EVIL (in their head).

Webcomics

 * Blip. Heaven is run by Knights Templar willing to ruin the lives of humans for the sake of preserving order. Hell is run by a genuinely nice guy, who nevertheless wants to plunge the world into chaos by amplifying the titular blip in God's plan. The real good guys aren't allied with either side.
 * Sluggy Freelance has Torg and his friends (the Good) sabotaging Hereti Corp, No Fun, and other ruthless organizations (the Evil) by working for the supervillain Minion Master (the Bad).
 * Rather than splitting the evil, Sinfest splits the good. God and Satan Are Both Jerks, but Buddha acts as a neutral figure in the conflict, ironically acting more "good" than the supposed good faction. (The protagonists themselves are all over the place—Slick in particular has declared allegiance to all three factions simultaneously.)

Web Originals

 * There Will Be Brawl: Red, Peach and Luigi are Good; Link and the remaining mob bosses are Bad; and Kirby,  is completely batshit evil incarnate.

Western Animation

 * Avatar: The Last Airbender's second season broke down into this, with Aang and friends being the good, Zuko being the bad, and Azula the evil. At the end of the second season Zuko would subvert the opportunity for a Heel Face Turn, but eventually do it in the third.
 * This is actually true for most of the show. In the first season, Aang and co. are the good, Zuko is the bad, and Zhao is the evil; in the first part of the third, the good and bad roles are the same, but with Ozai joining Azula in the evil. After Zuko's Heel Face Turn the system breaks down, though at the very end you have the Gaang as the good, Azula as the crazy yet pitiable evil, and Ozai as the stone-cold irredeemable sadistic evil.
 * Danny Phantom turned into this pretty early on and kept building on it. It used to be that Team Phantom was the good and the various ghosts he fought were the evil. Now, Team Phantom is good, Vlad and Valerie (along with a few more sympathetic ghosts) are the bad, and most of Danny's Rogues Gallery is the evil. By the end, however, Vlad is the evil and most of the Rogues Gallery is the bad.
 * The '90s X-Men animated series had one of the most memorable and sympathetic portrayals of Magneto ever to exist, out to defend mutantkind from its human oppressors, who were generally portrayed as pretty heavily bigoted. Of course the show couldn't have him be too evil with such a sympathetic cause, so he got thrust into Enemy Mine situations in all but his very first appearance against villains who were more evil than him at his worst.
 * Gargoyles did this often in the second season, most notably with Goliath and Xanatos (who may be the king of self-interest trumping morality, but isn't evil per se) teaming up against the out-of-control transformed Fox in "Eye of the Beholder" and the serial-killing Demona in the "City of Stone" arc. The Gargoyles spin-off "Bad Guys" was to examine a team of the show's lighter-gray characters working towards or away from redemption.
 * In The Spectacular Spider-Man Spidey is the good and most of his Rogues Gallery are the evil, with Tombstone as the bad- he's unquestionably a villain and a very ruthless one, but he sees his criminal empire as a business first and foremost and tends to avoid pointless cruelty. He (briefly) teams up with Spidey on a couple of occasions against the blatantly psychotic Green Goblin and Doctor Octopus.
 * It's not just him, either - Sandman, Black Cat, and (to a much lesser extent) Rhino are just in it for the money, and don't really go out of their way to hurt anyone (except Spidey himself, in Rhino's case). Sandman even gets to team up with Spidey for.
 * And Molten Man was working for the truly psychotic Green Goblin, but against his will - it was a pretty clear set-up for a Heel Face Turn, but the show was canceled just two seasons in.
 * In the fourth season of Kim Possible, Affably Evil Dr. Drakken and his Deadpan Snarker dragon Shego developed into "the bad". First by toning down their evil throughout the season and in the final episode by putting them in an Enemy Mine position against a race of Exclusively Evil alien invaders.
 * The Teen Titans had an alliance with Slade against Bigger Bad Trigon that lasted all of 2 episodes.
 * In Xiaolin Showdown there are varying degrees of bad and evil, while the Monks are unquestionably good, though they dip their toes in the darkside sometimes, there is Jack on the bad side but he wants to be the Big Bad. Chase could be considered bad also as he spends most of his time helping the monks while trying to fullfill his own goals. There is Wuya who is evil, but mostly harmless except when she reveals herself to be Not So Harmless, and finally Hannibal Bean who is very evil.
 * The Justice League temporarily side with the Legion of Doom against, Darkseid and his army from turning Earth into another Apokolips.
 * Luthor & company accidentally rescued Darkseid, and rather sensibly went straight to the League and explained there was going to be an alien invasion now and the planet needed saving, let us help. The League gave them a five-minute head start afterward.