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  • Jadestorm is a Wings of Fire fanfiction about a war between two tribes of dragons. It started when the SkyWing tribe had an epidemic, and the SeaWings refused to give them the antidote, despite not needing it themselves. The SkyWings launch an attack, attempting and failing to steal it. A few years later, under a new Queen, the SeaWings try to hand over the antidote, only to be rejected by the SkyWings, who claim it is too late for apologies. The PoV switches between a SeaWing and a SkyWing to show how both tribes are affected by the war. Each side is portrayed as being right and wrong in their own ways.
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  • Dungeon Keeper Ami is a highly unusual example, being something of a crossover-Fusion fic combo. What's interesting is that Grey-and-Grey is played straight, inverted, averted, and sometimes double-inverted. Sometimes all at the same time. This is accomplished by having the titular heroine and the current universe she resides in both play Black and White Morality very straight, but the heroine herself is bonded to an undoubtedly evil artifact. The forces of good, unused to such a situation, are reluctant to consider Ami as anything not-evil. The forces of evil consider her either an abomination, or the most brilliant case of evil overlording gone right.
  • Evangelion 303: Although initially the story pits a group of brave soldiers putting their lives in line to save the world and a shadowy terrorist organization, Grummancat warned that his story was going to be this. So, even though the Children are clearly heroic, Gendo is up to something, and Grummancat has hinted that things in Nerv are not as innocent as they seem. And Seele conspires against the USA because they regard it like a -literally- World Class bully... but they do not care for the loss of billions of lives and the collapse of world economy that would come as a result of the downfall of the "evil Empire".
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  • HERZ: The heroes are trying to protect humanity and their families, and in the name of that mission Misato has manipulated people and committed many shady actions she feels guilty about. SEELE is trying to liquefy all humans and merge their souls into a single being because they genuinely think it is something good.
  • Tiberium Wars portrays both the Global Defense Initiative and the Brotherhood of Nod in sympathetic light, with Nod being presented as desperate and angry and vengeful for the wrongs GDI has perpetuated on them, and GDI being presented as Well Intentioned Extremists who nonetheless are trying to protect the world and defend themselves against Nod aggression.
  • It should come as no surprise, but the crossover fanfic Renegade by the same author does the same thing, with the same factions. In fact, both factions are presented as protagonists, with the Brotherhood of Nod intervening in the slaver raid on Elysium and with Kane himself attempting to negotiate a compromise between GDI and the Citadel. Of course, Nod apparently stole the Tacitus on Eden Prime, which caused said conflict between GDI and the Citadel and allowed Kane to score points by negotiating said compromise, so it might have been part of the plan....
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  • Twenty Four The Musical, a fan-made musical of 24's second season lampshades this in the song "Dammit!" Jack Bauer sings that "Sometimes the rules can be gray," in justifying shooting Marshall Goren and then asking for a hacksaw.
    Jack: Get me a hacksaw, cut off his head!
    Mason: Are you crazy, Jack?
    Jack: Come on, George. He's already dead! I know this is drastic, it's all that we've got. Sometimes the rules can be gray!
  • In The Fairly OddParents fanfiction, Never Had A Friend Like Me, this is how Norm sees the genies vs. fairies arrangement. Norm has declared many times that he gets a kick out of tormenting masters by screwing them over, but he at least he doesn't pretend to be a saint. And while fairies do enjoy having godchildren and try to fill the gap their parents can't, he thinks the fact that fairies eventually terminate their relationships with their godchildren, not to mention their memories of time together is also pretty cruel. Granted he may have a point, considering Amanda his current master, and the most selfless girl he's ever encountered, is pretty horrified by the concept.
  • The universe created in the Star Wars/Mass Effect crossover Fractured zig-zags the trope. On one hand, it's pretty heroic to save a galaxy under attack but on the other, playing allies off each other (even unintentionally) tends to go over badly. Further, in a galaxy not ready for certain advanced technologies, even in face of Reapers it could be argued that the Trans-Galactic Republic got a little careless. Then the Republic Intelligence Service comes along in Origins to muddy things up...
  • Goddess Reborn Chronicle-naturally. Unusually, the players can fix it or create an apocalypse.
  • What Lies Beyond the Walls mostly focuses on two different factions. On one side is the Long Patrol, which is led by a badger who is a Jerkass Anti-Hero at best, and a bloodthirsty racist at worst. Most of the members of the Long Patrol are aware of how unhinged the badger is, but they usually just shrug off anything he does that they know is wrong, and some of the hares are just as sadistic as he is. On the other side is a Badass Crew of vermin corsairs led by Kurwin the Flayer. While some of them (Kurwin included) are merciless murderers and/or rapists, others are Affably Evil Punch Clock Villains, and a few members (most notably Stinkfoot) are Anti-Villains who only joined Kurwin's crew because they had nowhere else to go, and because Kurwin was nice to them and treated them like family.
  • The Revolutionary Girl Utena and Mawaru-Penguindrum crossover fanfic Seinen Kakumei Utena stays very loyal to both series in this regard.
  • Mentioned time and again in Eroninja that (almost) every faction is seeking to do what they think is right; whether it be for their family, their village/country, or the world as a whole. Shizune sums it up perfectly when discussing with Tsunade some of the morally shady things they've done compared to the morally shady things others have done.
    Shizune: We acted to preserve that which was important to us. Just like a village performs actions that might be viewed as wrong, but justifies them by claiming they are for the good of the many. In the end, there are no easy answers. Only those who act, and those who judge those actions based on how it affects them.
  • The revolutionaries in Star Wars Episode I: The Familiar of Zero seek to overthrow the monarchy, viewing the current government system as hopelessly corrupt, while the forces loyal to the crown wish to support Princess Henrietta who's a far more just ruler than her tyrant father was. Notably, both sides have their share of honest and corrupt men.
  • The Solar Empire and Luna Republic in the My Little Pony: Friendship Is Magic Fic Harmony Theory, despite having opposing ideologies and being on the brink of war, neither is particular worse-though neither is exactly as good as Equestria used to be either-they both have their good and their bad and are even hinted to be Not So Different. note 
  • Chrysalis Visits The Hague: While Chrysalis seems to be firmly (and proudly) rooted on the black side of things, the actual protagonists and antagonists of the story, the defence and the prosecution, have this kind of thing going on. On a broader scale, both the Equestrians and humans are in equal parts jaundiced, smarmy and secretive towards each other (though nominally well-intentioned in trying to bring justice to the Chrysalis matter).
  • It's not the Raptor DNA: One of the main conflicts in the story are the people who question whether or not it was right to forgive Elise despite her causing the deaths of countless people. She openly admits to her atrocities, and is trying to be better. In turn, there are humans and dinosaurs who stick up for her, and point out her traumatic treatment went into screwing her up. Her critics, however, are correct about how dangerous she is, and the deaths she caused. But their motivations and desires aren't always pure, with some people desiring to put her down, while others refuse to acknowledge her basic humanity.
  • In Earth 27, the conflict between Kherans and Daemonites is full of grey areas, since they're both ruthless alien empires, and while the Daemonites have a very good reason to hate Kherans, the Daemonites have no problem trying to take over Earth.
  • In Fallen Kingdom, the Koopa Empire has many shades to it, with some being bloodthirsty and others merely committed to the job, while others want to restore the Koopa Troop to its former glory and want to see the Empire fall. Similarly, the resistance has many shades of grey, with some hating all Koopas, others wanting to bring peace by any means necessary, and others, like Luigi, wanting to restore hope and bring the Empire down with minimal lives lost.
  • The un-linkable Porn with Plot series Monster Girl Encyclopedia surprisingly has this as part of its base lore, which various fanfics and stories can take in a variety of directions. Both sides of the in story conflict have their points and their failings: the titular monster girls are led by a Demon Lord who wants to end the conflict between monsters and humans, which she changed from more traditional monsters into many varieties of Cute Monster Girl some time after taking power with the intent of uniting both races as a single species. However her ideas of how to do this, being a Succubus and the series being, well Porn with Plot, means that the Anti-Monster Order faction has legitimate reasons to oppose her even without factoring in the fact that currently no monster males can be born (a problem said Demon Lord is working on) and a victory of hers too quickly could wipe out all sentient life. However The Order in turn tends to be Knight Templar to monsters even in fully peaceful situations and several of its defeats are just as much a result of its failures with its own people as much as it the power of the monster army: for example the order alligned city-state of Lescatie was made vulnerable to the Demon Lord's armies because of high taxes, invasive religious rules, and mistreatment of its human heroes. Fanfics set in the universe are capable of siding with either believably, with either, both, or neither side being able to be realistically held up as right or wrong.

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