Good Versus Good

""There are few wars between good and evil; most are between one good and another good.""

- Yang Wen-li, Legend of the Galactic Heroes

It's hard to create a story where both sides are fully sympathetic and yet in a real conflict with each other. But sometimes the authors manage to pull it off.

This is not when the characters on both sides are somewhat sympathetic, merely believe in their own actions without being fully sympathetic, or are in a temporary conflict by mistake. No, this is when both sides are unambiguously Good AND locked in a real conflict with each other.

This can be a philosophical struggle where Lawful Good and For Great Justice stand against the forces of Chaotic Good and For Happiness. In this case, the conflict is between a Hero Protagonist and a Hero Antagonist. It can also be when unambiguously good characters find themselves on different sides of a Grey and Grey Morality conflict. In either case, they are often reluctant to fight each other but can have a hard time understanding each other's point.

This trope is closely related to White and Grey Morality, but when that trope is played completely straight there can be no conflict beyond mere misunderstandings.

Compare with Both Sides Have a Point, Your Terrorists Are Our Freedom Fighters and Utopia Justifies the Means. Contrast to Black and White Morality and Evil Versus Evil. Might end in a Downer Ending.

Anime

 * X 1999 might to some degree be seen this way. The goals of both groups are reasonable. Saving the Earth from human destruction or saving humanity from extinction.
 * However, most of the Dragons of Earth could care less about saving the Earth.
 * Most arcs of Mahou Sensei Negima end up being this in some form or another, as almost every antagonist turns out to have a rather justifiably heroic motivation, although their methods are usually uncomfortably pragmatic. The exception, of course, is Tsukuyomi, who's just nuts and horny.
 * Magical Girl Lyrical Nanoha As is all about this. Literally everyone, protagonist or antagonist is trying to do what they think is right. The most evil character in the story is merely a Well-Intentioned Extremist. Hell, the resident Person of Mass Destruction summoned in the climax is not evil and quickly befriended. The best example however, is the ongoing fight between the TSAB (the protagonists) and The Wolkenritter (the heroic antagonists), which could be described as Lawful Good vs. Neutral Good. With the antagonists being the former.
 * Let's put it this way: in entire thing, closest thing to "evil" is Book of Darkness  Then again, her name ISN'T Book of Darkness to begin with...
 * In Suzumiya Haruhi, it is stated that the Organization, Koizumi's faction, and the time travelers, Mikuru's faction, are fiercely against each other. However, both sides are just out to maintain the status quo, and protect the titular character. Meanwhile, Yuki's faction are formless data entities, with their own inner power struggles and wars. On the whole, they prefer to maintain the status quo by not interfering except to maintain the masquerade, while trying to learn how Haruhi's powers work. As for the three agents, they have stated that should their factions go to war, they will stand by the SOS Brigade, breaking ties if they have to.
 * Good guys duel each other all the time in Yu-Gi-Oh!, but the struggle of Team 5D's versus Team Ragnarok really stands out. They may be dueling in a tournament match, but it's a full-on conflict of genuinely good-hearted heroes chosen by their respective gods to destroy the evil antagonists in the next round. Each side believes the other fights for good, but is also unworthy and incapable of defeating the Lords of Yliaster.
 * Since Hikaru no Go is about characters playing a board game, it's easy to find situations were the main character is playing against a fully sympathetic character. The conflict is serious since the characters are (or are trying to be) professional players and consider Go to be their main occupation in life. This is very apparent during the pro exams where Hikaru has to play against his friends Waya and Isumi who had helped him a lot in preparing for the pro exams. Only a very limited number of people can pass the exams, and every loss endangers the their chances.

Comic Books

 * The "misunderstanding fight" is a ubiquitous trope in superhero comics: X mistakes Y for an enemy and the punching begins. It's particularly likely to happen when two heroes meet for the first time. Any semblance of plot is just for show: this is largely an excuse to show the readers the spectacle of two powerhouses duking it out. Superman and Captain Marvel have had a lot of fights like this, despite being two of the most unambiguously good guys in the DCU.
 * The Civil War crossover in the Marvel Universe, where superheroes fought each other over a Super Registration Act. (At least, this trope was the intention - there's a lot of Depending on the Writer involved as to "who's right" and if/how much the other side gets demonized. Final score tends to rule that the pro-registration heroes were ultimately the "bad guys".)
 * The X-Men vs Avengers crossover back in the 80's, where the two teams were fighting over the fate of Magneto, who at the time had reformed and joined the X-Men. The Avengers--who generally turn a blind eye to the X-Men's actions since they know the mutants are heroes--wanted to bring a known terrorist to justice, while the X-Men wanted to protect their ally.
 * It's happening again in 2012 (as Avengers vs X-Men this time); now over Hope Summers, who is expected to become the next host of the Phoenix Force. The X-Men again want to protect one of their own, the Avengers justifiably see the Phoenix as a potential threat.
 * Just prior to the latter scrap with the Avengers, the X-Men (mainly Cyclops and Wolverine) fought amongst themselves in Schism over whether or not the younger members should be involved when the group faces life-or-death battles.
 * Wonder Woman gets this a lot, since she explicitly has no code against killing, and this occasionally brings her into conflict with Superman and Batman. A prime example is the graphic novel The Heketeia, in which Batman is the primary antagonist.

Film

 * In probably the only true manifestation of this trope, the two main characters from The Iron Monkey are both doctors and expert martial artists. It's no surprise that they end up fighting side-by-side at the end, but for most of the movie, one is motivated by fighting the corrupt government, while the other is motivated by preventing said corrupt government from holding his son hostage by catching the other one. Neither side has the moral high ground.
 * T-800 versus the police in Terminator 2:Judgment Day. Arnie wants to ensure the destruction of Cyberdyne, whereas the police merely do their job, stopping an apparent terrorist act.
 * The conflict between Woody and Buzz in the first Toy Story.
 * Unfortunately a big downer in The Matrix. Neo and his allies frequently kill/injure law enforcement agents, who are simply not aware being part of the Matrix.
 * They are also extremely ruthless about it; in the first movie especially they don't so much fight law enforcement officers as massacre them, particularly in the Hallway scene (Neo even machine guns a guard who was reading a newspaper). Morpheus gives their stone cold philosophy on the subject early on- everyone they are trying to save is plugged into the system, and "that makes them our enemy". Its actually quite chilling when you consider the implications of that, since in theory they are willing to kill even civilians to achieve their end. In the sequel, in fact, they do just that, when they blow up a power station and kill everyone who stands in their way, or beat them up and leave them to die
 * The Fugitive has US Martial Sam Gerard, whose job is to capture murder suspect Richard Kimble. Richard Kimble is innocent however, and his job is to find the real murderer and clear his own name.

Literature

 * In A Dark Wood by Michael Cadnum, a retelling of Robin Hood from the perspective of The Sheriff of Nottingham, a good man who distastefully upholds brutal laws, yet is eventually able to recognize that his outlaw adversary is also a good man.
 * Yeoman and Popinjay hate each other in the Wild Cards books, specifically due to the fact that Yeoman is a mass murderer (of evil people) while Popinjay is a private detective who nevertheless views such things as monstrous.
 * Honor Harrington, between the fall of the Committee and the Battle of Manticore. It eventually gets really frustrating (not to mention Tear Jerking) to watch good, sympathetic characters killing each other (especially ).
 * Ender's Game. Poor communication eradicates.

Live-Action TV

 * Buffy the Vampire Slayer and her initial clash with the solders of the Initiative - especially Riley - is like this. It gets gray and grayer once we learn more about project 314 and Maggie Walsh' plans though.
 * Her initial run in with Sid the puppet Demon Hunter was the result of a misunderstanding (her power made him think she was a demon, and the evil puppet thing is too much a cliche for her to think it was anything else).
 * Angel The fight between Angel and Spike in the Season Five episode 'Destiny'. Both have a soul, both want to drink from the cup of perpetual torment - whoopsie, someone got staked.
 * In the second season of The X-Files we finally learn that Skinner is not as cold-blooded and ignorant as he appeared to be at the end of the first season, but that he is merely forced by the CSM/the Man to give Mulder a hard time.
 * Supernatural addresses this in the second season arc involving Gordon Walker. He is a hunter, a relentless one, but only interested in killing vampires/demons - at first.
 * The re-imagined Battlestar Galactica has the conflict(s) between Commander Adama and President Roslin, Starbuck vs. Kat, Starbuck vs. Apollo, Everyone vs. Helo - and a lot more. Most of them take place between two parties who want the best for the fleet.
 * For the first half of Person of Interest's first season, the two sides were John Reese and Harold Finch, vigilantes stopping violent crimes before they happened, and NYPD Detective Carter, their Sympathetic Inspector Antagonist.

Professional Wrestling

 * Good vs good is something that is fairly uncommon for the simple reason that when you have two good guys who are equally popular, the crowd is divided between them. This generally makes bad TV, so it is avoided if possible. If you have two faces, generally one guy turns heel, at least for the duration of the feud.
 * The Ultimate Warrior vs Hulk Hogan, culminating at Wrestlemania 6 in a title-against-title match.
 * The Rock vs Hulk Hogan, although in a special case, Hulk's popularity was so great that the Rock turned heel mid-match, only to turn back afterwards.
 * Hulk Hogan was actually a Heel in that match as a member of the nWo. He didn't turn face until after the match when he shook The Rock's hand and both fought off Kevin Nash and Scott Hall.
 * TNA recently had Ken Anderson, Jeff Hardy and Kurt Angle go into a three way for the TNA Heavyweight title; all were faces, but Jeff Hardy turned heel at the conclusion with the reveal of the Immortal.
 * Stone Cold Steve Austin vs The Rock at Wrestlemania X7. At least until Austin sold his soul to Vince McMahon.
 * Though they were in Texas at the time, so Rock was the Designated Villain for the match, even after Austin turned. It wasn't until the next night that he built any real heat as a heel.
 * The Rock still wasn't the "villain" per se; the crowd just didn't cheer for him, at least not at first. The match is actually a good example of why this trope is so rare, since the fans didn't seem to know how to react to the Rock, since against anyone else, or in any other state, they would be cheering for him too. Also, near the end of the match when it was clear what side Austin was on, the crowd did start cheering on The Rock, and even gave him a massive ovation the last time he kicked out of Austin's savage beating.
 * Wrestlemania XII was unique in Wrestlemania history in that the two wrestlers who faced each other for the title in the main event were not feuding, were not presented as having any sort of bad blood, and in fact got along with each other extremely well, both openly declaring on a number of occasions that they enjoy working with each other and look forward to the challenge. It wasn't even like Hogan vs. Warrior where the script went out of its way to present neither of the enemies as being fully in the right or being arrogant: they weren't enemies. There was no feud at all and no moral high ground to be seen. Rowdy Roddy Piper even used his in-ring charisma at one point to influence the crowd into not booing previous Heel Michaels. They did everything they could to show that we're not necessarily supposed to be rooting for either man, and instead focused on selling the main event based on its own merits: an hour-long "iron man" match.
 * Also counts as Hilarious in Hindsight The two "not enemies"? Bret Hart and Shawn Michaels, who developed real heat with each other after this match due to the winner's instance that the loser get out of the ring so he could celebrate his win. After that, the two had massive animosity towards each other that burnt for over a decade before they sussed it out.

Tabletop Games

 * When a non-evil party goes up against non-fallen celestials in Dungeons and Dragons, it's this trope.
 * Discussed in Champions of Valor. To paraphrase the author, good-on-good violence is unlikely to occur in FR since good-aligned characters and nations are likely to have bigger fish to fry.
 * In Talisman, characters of the "Good" alignment are supposed to fight each other just like everyone else, and in the endgame they HAVE to fight each other.

Video Games

 * Applies to pretty much every Fighting-game. The results and causes may vary, but at one point or the other, 'Good characters' will battle 'Good characters'.
 * The Soul Calibur series. With the exception of three or four characters, they're mostly heroes who will battle whoever it takes to obtain Soul Edge.
 * The Super Smash Bros. series. Especially the N64-version. Not a single 'evil' character.
 * In World of Warcraft, the main conflict between Alliance and Horde is Grey and Grey Morality, but it contain pockets of Good Versus Good as well as Evil Versus Evil. When it's Black and White Morality, the "white" side is sometimes the Alliance and sometimes the Horde.
 * Very, very common in the Tales (series), although the good side not controlled by the player is generally more "ends justify the means" and willing to employ genuine evil in their pursuit of noble goals.
 * In Metroid Prime Hunters, at least one rival (Noxus) is unambiguously good. Samus and he fight anyway.
 * Spire also fits this category, since he's hoping to revive/find out more about his species.
 * The conflict between Thorndyke and the Nereids in Soul Nomad qualifies. Thorndyke wants Feinne undisturbed to prevent the situation from potentially getting much worse. The Nereids want to kill Feinne to solve the crisis of the World Eaters.
 * Ar Tonelico 2 (Video Game). Where do we begin?! While people do truly horrifying things to each other, not a single faction is doing it out of selfish interest. Each one believes that they are doing the right thing for the world and the people who live in it, and each of them have their points. Even the Mad Scientist Big Bad only wish to stop the suffering of the people , and she does this out of a sense of responsibility for failing to provide a paradise on earth long, long time ago.
 * One can say that the point of Metafalica is that people are basically good, and they need to work together. Metafalica is created when two maidens join their hearts, after all.
 * Related to Color-Coded Multiplayer many games with multiplayer options only let you play as the good guys or Palette swaps of the main protagonist.
 * The original Halo's multiplayer consists of Spartans (who are on the same side in the game's story). The sequel adds the enemy Elite aliens, but only after they had done a Heel Race Turn.
 * Touhou Project games have never had any true villains. Just a lot of spoiled, lonely, stir-crazy, lazy, playful and/or protective characters. The only real life-threatening situation in a long time has been the last stage of Subterranean Animism where defeat would have cause the protagonist to fall into the Hell of Blazing Fires.
 * And that was only because the final boss (Utsuho Reiuji) went crazy with power. Reimu (the player character) snapped her out of it.
 * Actually, it seems that the latest game, Ten Desires, has several enemies who are somewhat evil.
 * Played fairly straight in the first Advance Wars game. The vast majority of the Commanding Officers are all pretty much morally upright people who are entirely convinced that they're fighting for justice. This does not stop them from getting in drawn out territorial conflicts throughout most of the campaign.
 * in Neverwinter Nights 2 features celestials versus paladins, and potentially paladin versus paladin.

Western Animation

 * Candace's constant attempts to bust Phineas and Ferb although it can also be viewed as Law Versus Chaos or Chaotic Neutral versus Good depending on one's perspective of Candace and the boys.