Cass: NCR's my country, and I support it. Anyone says otherwise... I'll feed 'em my knee. I know which side of the firing line I'm on in the Mojave, just so you know.
The Courier: There's a "but" in there.
Cass: Yeah, there is. I'm not some blind, flag-saluting, do-as-they-will NCR lover. They're like family, but let me tell ya what family means. You ever had a brother? Some dumbass younger brother, say, who knocked up the pastor's daughter, can't hold down a job and his home-away is a jail cell? That is NCR. Their compass is spinning. All the time.
The character is a noble, or at least decent, soldier, who doesn't like the policies of their nation and/or state, but fights for it anyway. This person is loyal to their nation, not its leader. Exactly how noble or decent someone can be while helping their organisation do questionable deeds because it is "their duty" varies depending on the specific character and their actions. Moral Dissonance is something anyone can have and evil leaders are very good at promoting and exploiting nationalism, particularly when it comes to inter-national conflict and war. One does often wonder why someone so honorable fights for an evil cause rather than deserting. At worst, this sort of thing can lead to the "I was Just Following Orders" defense. More positively, it may result in them questioning their Blind Obedience and defecting or rebelling.
The title is a common variation from a quote from the USA's naval commander Stephen Decatur...which is all too often taken out of context. For immediately beforehand, Decatur had toasted: "To our country! In her intercourse with foreign nations, may she always be in the right." Later, the USA's Senator Carl Schurz gave his own interpretation of the statement: "My country, right or wrong; if right, to be kept right; and if wrong, to be set right." This latter take, along with similar anecdotes from others, has also come into prominence in how both nationalism and patriotism are portrayed.
No Real Life Examples, Please!. Which country is "wrong" or "right" is extremely subjective because widespread, unconscious belief in the principles of nationalism makes people believe that their chosen nation is always 'more right'. Let's not start up a Flame War over this, thanks guys. (Even though the trope doesn't have to be only about who is "right or wrong" among the country leaders, but about unquestioned or blind loyalty of (mostly) soldiers towards them due to patriotism, be it genuine or indoctrinated, including historically)
Compare Realpolitik, My Master, Right or Wrong, Lawful Stupid, Just Following Orders and Tautological Templar.
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Most of the cast of Fullmetal Alchemist are soldiers of the evil Amestris. The average soldier only cares about fighting for their country and the good of the people, it just so happens that it involves the occasional massacre. Roy Mustang's entire storyline is about his plan to overthrow Fuehrer King Bradley, who, like the Gundam example below, is based off of Hitler. Roy can then become the new leader so he can bring peace to Amestris.
Ramba Ral is a particularly stand-out example. Despite the fact that the Zabi family had his father killed as part of a nasty Cycle of Revenge that began with the death of Zeon's former leader, at the end of the day he's still a Zeon soldier and they're still the royal family (it does help that he works for the comparatively decent Dozle Zabi, who probably had nothing directly to do with the whole mess). This comes back to bite him when he comes to Earth to fight the Gundam, since the Earth Attack Force command, under Kycilia's authority continually stiff him on supplies and support, possibly because they don't believe he could really be that loyal, more likely due to simple Jurisdiction Friction, and he continues to soldier on with what he knows to be a suicide mission regardless.
Many characters from various Gundam series are examples, though countries seldom matter and it's often loyalty to other institutions, e.g. Gundam 00 has Sergei Smirnov, who dislikes actions such as the HRL's Supersoldier project or the world government's A-Law's actions, but he stays loyal to them.
Except that he quite openly schemes behind the A-Laws' backs and leaks intel on them to Celestial Being.
It's a given, considering the series, but several countries in Axis Powers Hetalia are portrayed as this, especially WWII Germany, who expresses open disgust at some of the orders he's been given, but has to follow them anyway. Or Russia's growing anger at Stalin despite being more or less fine with communism. Considering that all of the characters are personifications of their countries. They aren't bound to a particular government, leader or ideology as they represent their people as a whole. Which includes their ideas/cultures/beliefs/what-have-you in general. Plus, autocratic governments can hardly be considered representative of their people in the same way as democratic ones, so it makes sense for their countries to hold different opinions to their rulers - and also to be unable to stop them. Dictators don't hold elections.
The Britannians in Code Geass, even if their rulers oppress others and promote racial supremacy.
Also, Suzaku, who fights for the lawful authority of a region, even if it he obtained that authority by brutally conquering his own country.
Gajeel of Fairy Tail is this, which is what makes the members of Fairy Tail eventually accept him after the events of the Phantom Lord Arc. Gajeel is also majorly Ax-Crazy, which translates to something like having a really mean guard dog that will do everything possible to protect it's owner.
Bleach: Byakuya Kuchiki sided with the law when his sister Rukia was arrested and scheduled for execution. Despite disagreeing with the situation, he was bound by his social position, his military position and a promise he had once made over his dead parents' honor. As an aristocratic role-model for society in general, he was trapped by the fact that he could not expect others to uphold the law if he broken the law whenever it personally inconvenienced him. As a captain in the Gotei 13, he was expected to obey the orders of the Central 46 without question or hesitation. And, in his past, after having thrown his family into chaos by breaking the rules to both marry a commoner and then honour her deathbed request to adopt and protect her sister (Rukia) as his own, he made a promise to his parents' tomb that he would never break the rules again. Rukia's execution forced him to choose between those two conflicting vows but the sheer weight behind the vow to uphold the law meant that was the vow he had to choose no matter what his personal feelings may have been about it.
Yamamoto was also this. Ukitake was Rukia's captain and determined to protect her no matter what and Kyouraku found the whole situation suspicious and wanted to halt the execution until it could be investigated. Both captains broke the law by refusing to uphold the decision of the Central 46 without question and sealing the execution weapon to ensure Rukia couldn't be executed. Yamamoto, incensed by their betrayal and making exactly the same argument Byakuya had made to Ichigo (that society takes precedence over the personal), proceeded to engage them in a fight that would have been to the death had the truth about Rukia's execution not come out in an extremely timely fashion. His personal opinion on the matter of Rukia's execution is never revealed, to him, it didn't matter if it was right or wrong. Upholding one's duty was the only 'right' he was interested in.
Gladiator, of the Shi'ar Imperial Guard from X-Men, has explicitly stated that his loyalty is to the Throne, regardless of who's holding it (ultimately, he turned out to be very right to support Deathbird: she turned out to be a very capable majestrix. The mad emperor D'Ken, on the other hand...), going as far as serving Vulcan while showing distaste for having to fight Lilandra. Ultimately, however, Vulcan's actions prove to be so far beyond the pale that even Gladiator can't bring himself to serve him.
As of the War of Kings event, Gladiator is the one holding the Throne.
Eric Finch, Chief of New Scotland Yard in the V for Vendetta graphic novel. Helping to keep his country afloat in its hour of need, he tells the Big Bad his disdain for the fascist Norsefire Coalition right to the man's face. The Leader replies that it's a measure of his respect for Finch's craft that he's still alive to say that. In the end, Finch decides that upholding such a regime isn't worth the price.
Former Captain America USAgent (as opposed to the actual Captain, whose duty is not to whoever is elected to lead America, or the organisations formed by America, but the ideals of America), and also the Iron Cross, who fought for Germany in WWII for precisely these reasons.
Hans von Hammer, protagonist of DC's Enemy Ace feature and WWI pilot for Germany, especially in Garth Ennis' War In Heaven (WWII) version. However, when he discovered the Nazi death camps of the Final Solution in the final days of the war, that was the last straw for him and he led a mutiny with his unit.
Subvert in the Dave Gibbons/Will Simpson re-imagining of 2000AD series, Rogue Trooper. The Genetic Infantry are shown to be an elite band of highly-motivated, unshakable soldiers, but they show no interest in the cause which they serve. Their motivation is drawn from genetic and psychology conditioning and a fierce bond of brotherhood.
One version of the Unknown Soldier, a bandaged character from DC Comics. The long-lived soldier snapped upon seeing a Nazi concentration camp. He decided that since the USA fought against something this horrible, whatever they fight against is the right thing to oppose.
This is what happened to the character of Superman in The Dark Knight Returns, though that was not in canon, where he's frequently refused to do favors for the U.S. government if he feels they are wrong, especially when Lex Luthor was President. His attitude towards the city of Metropolis however, is closer to this trope.
Superman doesn't believe in My Country, Right or Wrong when it comes to governments, he will usually follow the wishes of the American people, even if he doesn't agree with them. For example, in the "Public Enemies'' arc of Superman/Batman, he says:
The world will never know how I struggled with the decision to stay out of the electorial process. Should I have gone on television and told the voters not to elect this man? And what then? If I use my influence — my character and my reputation — to tell people how to vote, what does that make me? I choose to fight for Truth, Justice and the American Way. And for all it's flaws, American democracy does work... The United States doesn't need me to dictate, or worse, deprive her people of that most precious gift. The freedom of choice. Even when I knew in my heart that choice was wrong.
In The Masks We Wear Zuko refuses to believe that anything the Fire Nation did is wrong, and as such considers the mere thought of helping the Avatar and overthrowing his father as treason.
This is a major theme throughout Birds of a Feather. Many major characters struggle with the implications of remaining loyal to nations whose actions become increasingly extreme, and both ZAFT and the Earth Alliance are portrayed as having both war criminals and dedicated soldiers fighting for their countries in their ranks. A handful decide that loyalty to their nation is not the same as loyalty to their military, and decide to break away and try to set right their nation.
Seen in Das Boot, where the submariners, except for the 1st Lieutenant, disliked the Nazis and were just doing their job. Arguably necessary for the audience to be able to sympathize with people fighting for Nazi Germany, and to some extent Truth in Television, as many in the Kriegsmarine resented the fact that the Nazi hierarchy paid more attention to their army and air force. (A purported but plausible quote from the Führer in real life: "I've got a Nazi air force, a conservative army and a communist navy.")
Several of the more sympathetic Havenite characters in the Honor Harrington stories qualify, especially before the second Enemy Civil War. A couple did switch sides but most just tried to stick it out - and some did manage to make improvements in their own countries by doing so. As time has gone on and the government changed, Haven is no longer an obvious "bad guy".
Indeed, Cachat's The Plan in "Fanatic" depended on the majority of the Havenite officers and enlisted being decent people, including many of the State Sec officers (consider that State Sec is normally presented as Lawful Evil, and only mildly lawful at that). A man in Cachat's position would be in a position to guess which way those particular State Sec officers would move.
Cachat himsef subscribes strongly to the "if wrong, to be set right" interpretation, stopping shy of nothing to do so.
Another Havenite example was Amos Parnell, the former head of their space navy. Thought executed, he was discovered and rescued from a prison planet, and despite having every reason to utterly hate the current government of Haven, refused to provide intelligence that would directly assist the Manticorans in battle against Havenite forces. However, he does testify about the coup and helps destroy the new government's prestige.
In contrast, he convinces the much younger and more idealistic Havenite officer Warner Caslet to defect. When Caslet attempts to invoke this trope, Parnell shuts him down. "Son, you don't have a country anymore." In Caslet's case, recent circumstances outside his control had guaranteed that Caslet would be executed or disappeared if he returned to Havenite territory.
Thomas Theisman articulates this thought several times when considering Alfredo Yu, his own mentor who defected, and Warner Caslet, one of his subordinates whom he considers an honest, integral man who wanted nothing more than to defend his nation and was driven into defection. Theisman understands and empathises with them both, while still deciding that he cannot follow in their footsteps because he is loyal to the Republic, if not to its leadership. Theisman himself, however, is someone who takes the full Schulz quote as his motto, including the part about "if wrong, to be set right." At the end of Book 9, he shoots Citizen Chairman Saint-Just and restores the old Republic.
Many imperials in the Star Wars universe use varying degrees of this trope. Some desert right away after Battle of Endor. Others remain loyal until the interim government implodes. Some defect or desert after they become sickened by their commanding officers or realize that the Empire has lost unity.
Pellaeon remains loyal to the person who has the most legal claim to the government and later commands the Remnant. However, as time goes on he realizes that the Remnant must change its racist policies to survive.
Günter Bischoff, the U-Boat captain in Cryptonomicon starts off like this (he's definitely not a Nazi), but ends up just looking for a way out of the whole thing.
Oberst Kurt Steiner from The Eagle Has Landed. He actually risked his life trying to save a Jewish girl from death. He is then court-martialed, along with a platoon of his men. They are then given the job of kidnapping Churchill. One of them rescues a local girl from a water wheel and is killed in the process. So it is obvious that they are good guys, yet they still fight for Nazi Germany. In an aversion, it is hinted that Steiner hesitates when he has a chance to shoot Churchill because he knows it is wrong, and is himself then shot and apparently killed.
Soldier X might fit here. The main character talks about how, as a teacher, the new students always stare at him because he is missing an arm. When they inevitably ask about it, he reveals that he lost it in WWII and someone always comments "it had to be done". However, the main character was a conscript in the Wehrmacht (although it is a little more complicated...).
In The Three Musketeers, Rochefort is depicted as an honourable opponent of the eponymous musketeers. Although, there, it's more a case of "My Boss (Cardinal Richelieu), Right or Wrong", as both he and the musketeers are loyal to France.
In Monstrous Regiment, this is the attitude that Corporal Strappi preaches. Sergeant Jackrum also follows this, but at the end, retires to find out, as he put it, "what I've been fighting for" his entire life.
Eric von Shrakenberg of The Draka takes this trope to a whole new level, given that the country he is fighting for is the Domination of Draka, which makes Nazi Germany look tame by comparison. Although he views the Draka ideology and society as a cultural dead-end, he is arguably the single most important individual in Draka history, playing a key role in both the Eurasian War and The Final War.
In Ruled Britannia, an Alternate History novel where the Spanish Armada succeeded and occupied England, William Shakespeare (Yes, the William Shakespeare) admits that, if given a choice, he probably would choose to follow the Roman Catholic traditions of Spain as opposed to the Protestant teachings of England, but he refuses to let these traditions be forced onto the country at gunpoint. Thus, he helps launch the rebellion that topples the government of Queen Isabella and frees the imprisoned Queen Elizabeth, even if that means he will need to become a Protestant again, because, at least then, it would be by England's choice.
Also a recurring theme in Turtledove's Timeline-191 series with citizens in the Confederate States, since they are the analogue to Germany. Clarence Potter is the most notable - he despises Jake Featherston personally and feels his temperament is ill-suited to the Presidency. But he also saves Featherston from a black assassin and a planned military coup, on the grounds that eliminating him would only lead to the CSA being conquered by the more powerful U.S.
A minor recurring theme in the 1632 series, as we repeatedly see people from "enemy" nations who recognize based on the foresight/hindsight provided by reading the uptime history books that their countries are in the wrong at LEAST practically if not morally (such as upholding serfdom), but serve their country regardless even when rulers fail to recognize the warnings.
Biggles antagonist Erich von Stalhein: "Germany meant more to me than Hitler ever did. It still does." He is quite explicitly a German nationalist, and seems listless whenever not serving its interests, even working for the Soviets, despite being a monarchist to the core himself.
In Darkness at Noon, Rubashov's background was that of a faithful enforcer of the Party line who publicly upheld the principle of the Party's infallibility, though privately admitting that it had turned against the principles of the Revolution that he had fought in. Ivanov questions why he does not see himself as a traitor.
In the novel Red Storm Rising, Alekseyev serves the Soviet Union, all while having private doubts about whether what the country is doing is legitimate or worthwhile, particularly staging a bombing of the Kremlin that killed several children early in the novel.
Captain Laurence from the Temeraire series is deeply devoted to Britain, and his sense of duty is what constantly drives the plot- he hated the thought of taking on a dragon, but did it because he thought it was right. However, he finally draws the line when he hears of a British plan to infect every French dragon with a fatal disease, and let to spread and kill every non-British dragon in the world despite them being sentient beings, which finally prompts him to turn traitor.
Bryce from Max Headroom is loyal to the TV company Network XXIII, to the point of trying to kill Edison Carter in the first episode. But Bryce is doing it only because it was ordered of him, and he bears no genuine malice. He just wants to play with computers.
This is only true of Bryce in the American version, however; in the original British Made-for-TV movie, Bryce is not only wholly unsympathetic, but killing Carter is his idea in the first place.
This trope is Gul Dukat's explanation for switching his allegiance to the new, democratic Cardassian government in an earlier season. In a rare moment of direct honesty he admits that this quasi-Heel-Face Turn took place shortly after it became obvious that the old regime was going to lose.
Dukat: As a loyal officer of the Cardassian Military, I am pledged to serve the legitimate ruling body of the Empire, whoever that may be
Sisko: In other words, you saw which way the wind was blowing and switched sides
When Garak is ordered to kill three dissidents and Quark (who's helping them escape Cardassia), he does admit to Quark that he has to carry out the verdict of the Central Command even if it's against his better judgement to follow those orders. Subverted in that he eventually makes the decision to defy the Central Command and help the dissidents escape.
Really, My Country, Right or Wrong is the guiding principle for all Cardassians, all the time. The problem is that each of them has a different idea about what's good for the empire, ranging from "I should be the ruler because I am obviously the right man for the job" to "The Cardassians need to own up to the crimes in our past."
The Jem'Hadar are bred to be unquestioningly obedient to the Dominion, even obeying orders to go to their deaths because "it is the order of things."
A variation of this is spoken of by Jonathan Archer in Star Trek: Enterprise in the Mirror Universe episode "In a Mirror, Darkly", where he claims that Starfleet officers are loyal to the Terran Emperor, not the person currently occupying the throne. All one has to do is to successfully overthrow the government and name oneself Emperor, and the military will support him or her.
In the Babylon 5 episode "Endgame", General Lefcourt leads the ships loyal to the Clark regime. As he puts it, "I'm from the old school: a soldier doesn't take up arms against his own government, no matter how justified you feel doing it." That said, when President Clark sets up Earth's defense grid to scorch the planet rather than let Sheridan win, Lefcourt destroys the last orbital defense platform that Sheridan's fleet couldn't reach. He only did so after Clark was dead, and thus no longer President; given Luchenko's rise to Presidency, presumably Earthgov has an analogue of the Twenty Fifth Amendment. It turns out that many members of Earthforce had that same mindset, including Babylon 5's later CO, Captain Elizabeth Lochley. , 
Lefcourt's mindset does invite the question whether he would have followed an immoral order and allowed the orbital defense grid to kill millions of people. The real-life section of Screw the Rules, I'm Doing What's Right has an example where the Prussian officer was expected to violate an order.
Many officers refused to obey immoral orders during the Earth Alliance Civil War. , , , 
This trope gets a very thorough working over through the course of the show, particularly in the latter three seasons. The fifth season addition to the cast of an Earth Force Captain who refused to join Sheridan's faction in the civil war adds an ongoing layer of character friction.
Captain Sheridan himself also qualifies. Clark appointed him to command the station because by all appearances he was a staunch loyalist. What Clark didn't count on was that Sheridan was staunchly loyal to the Earth Alliance Constitution, rather than being loyal to the government that was violating that Constitution. He ended up fulfilling the second part of the quote: "if right, to be kept right; and if wrong, to be set right."
On Highlander: The Series, Duncan fought for the North in the Civil War. He met another immortal who fought for the South. He said that the other immortal was on the wrong side; the other immortal acknowledged that he was, but said that he had made ties with his neighbors and friends and didn't feel like he could turn away from them.
In the Doctor Who episode "Doomsday", Yvonne Hartman (leader of Torchwood in 2007) did her duty "for queen and country" even after being upgraded to a Cyberman.
Rankol in the 2007 Flash Gordon, who explains to Princess Aura, before his apparent Heel-Face Turn, that his loyalty is to the ruler of Mongo - whomever that may be.
In a very early Mission: Impossible episode, "The Reluctant Dragon," the main villian, played marvelously by character actor John Colicos, is well aware of the evils of his country's oppressive policies, but carries on as Security Minister because he's loyal to his country, and insulates himself in cultural pursuits. It's not hard to imagine that things would be much worse with someone else in his place, and he ends up being probably the most sympathetic villian in the series' history; as he lies shot at the end, he even generates a degree of compassion and respect from Rollin, who takes time to help staunch the bleeding before making his escape.
Zorro, in the 1957 series, is shown fighting for his beloved Spain, even against revolutionaries... even though it is repeatedly shown to be a totalitarian regime that cares more about its own petty wars than its citizens. The sequels made sure to rectify this.
As do Levellers in a few of theirs, most interestingly, in England My Home
Oh, what happened to
My green and pleasant land?
German punk band Die Toten Hosen's "Tausend gute Gründe" lists "a thousand good reasons to be proud of this country" only to admit that at the moment, they can't actually come up with a single one.
A common depiction of the Imperial Guard in Warhammer 40,000 has very strong tones of this, especially when they're the antagonists. Otherwise, they actually believe what they're doing is right in itself.
One quality in Shadowrun is named this. In exchange for swearing a fanatical loyalty to your faction, to the point of that betraying them in any way is unthinkable, a character receives the ability to ignore damage penalties in combat.
Anatoly Sergievsky of Chess, a rather timid and awkward man hounded by the press as to why he still supports his country of Soviet Russia. He proceeds to sing "Anthem":
Anatoly: When no flags flew, when no armies stood, my land was born. And you ask me why I love her? Through wars, death, and despair? She is the constant we who don't care. And you wonder why I leave her? But how? I cross over borders but I'm still there now. Let man's petty nations tear themselves apart! My land's only borders lie around my heart!
Papers, Please. Although the first choice players may take is to simply follow the law, is it worth following laws when the people upholding them are more corrupt than you? Is it worth taking that bribe if you know you're going to be better off than if you didn't?
The Fire Emblem series in general does it too many times to count.
Camus the Sable from Shadow Dragon is somewhat tragic as he was a kind-hearted and brilliant man but valued his country above all else. He exemplifies the trope well enough that in the fandom, the "Camus Archetype" refers to antagonists with sympathetic personalities and motives who nonetheless cannot be convinced to join your army and must be defeated. Fortunately, he survives and is recruitable in the 3rd game.
Eldigan in Genealogy of the Holy War was king of Nordion, best friends with Sigurd and Quan, and the brother of Princess Raquesis, who fought because Agustrian usurper King Chagall threatened to smear mud on his name. And if you don't fight him and, instead, get Raquesis the Earth Sword, Eltshan will still be executed by Chagall and the Cross Knights will continue to battle you.
Ishtar from the same game's second generation. She's kind hearted enough to be the best friend of Teeny/Linda, despite Ishtar's mother abusing them, she seriously questions the Child Hunts promoted by her country and tries to minimize the damage as best as she can, but she's too duty-bound with the honor of her family and country (and being in love with pre-possession Julius), in which Seliph's army has caused many casualties on, that she cannot be recruited and made her last stand in the name of those she's bound to, dying in process.
In Sword of Seals, Miledy's lover Gale is a Wyvern Lord (and subsequent Dragon General) whose allegiance belongs to King Zephiel and General Murdock, while Miledy fights for Zephiel's half-sister Guinevere, who is on a different side of the conflict. Gale tells her that he cannot be with her, despite spending so much time together. He also tells Miledy's brother Zeiss that, no matter what, they must fight. What makes it worse is that Gale is considered dead even if you don't kill him.
Another Sword of Seals example is Brenya, who is portrayed much like Selena would later be. Despite King Zephiel's death in the last chapter, she still carries out his orders, even if it means death. Even after being told that surrender is an option, she won't take it.
And again in Sword of Seals is the Etrurian Generals, especially Douglas, since he downright refuses to join you even if you talk to him with General Cecilia, General Percival, Vice-General Klein, AND his adopted daughter Lalam/his liege Prince Mildain (Elphin). He only joins you later when Etruria officially accepts your army, AKA when you defeat the chapter with Douglas still alive, allowing you access to 16x.
Vaida in Blazing Blade was a noble soldier and former Dragon General of Bern who was forced to desert along with her subordinate Heath, because her group attempted to prevent the murder of innocent civilians, which had been part of a plot by a Bernese general aiming for grandeur and promotion. She was recruited in the Shrine of Seals battle so as to keep loyal to her liege, Prince Zephiel. More specifically, she states that she serves Bern, and joins Eliwood's army because they saved the life of Prince Zephiel, who is the future ruler of her country. She embodies this trope perfectly whilst employing Loophole Abuse out of a sense of honour.
General Eagler from Lyn's Tale. Especially tragic case because, if Sain and Kent (and a civilian in a nearby house) are to be believed, he might have been forced to fight by having his family taken into custody by Lundgren.
Selena in Sacred Stones, who is portrayed entirely sympathetically but remains loyal to Emperor Vigarde to the very end.
Path of Radiance actually hangs a lampshade on this when Ashnard tells Bryce, the last of his Four Riders, that yes, he is a complete bastard (the specifics are technically spoilers, but everyone who played at least halfway through can probably figure them out). Bryce is appalled at what Ashnard says but is still loyal enough to go out to die, and Ashnard breaks out into a fit of laughter, mocking his notion of chivalry.
In the following game, General Levail of Begnion can be seen in a similar situation as Bryce: he knows of how corrupt the Begnion Senate is (he was the commander of Vice-Minister Lekain's personal army) and wishes that it isn't so, but he still fights you out of loyalty to Zelgius, AKA the Black Knight.
Zelgius himself may count. Zelgius is loyal to the Begnion Senate only because he's loyal to Sephiran, who wants him to help incite a war that will swallowing the world, which is the same reason the Black Knight served Daein.
Micaiah fits this trope perfectly in Radiant Dawn. She is willing to side with the Begnion Senate in fighting the Laguz alliance - despite the fact that she just led the charge to free Daein from Begnion control, that her home country needs to rebuild, and that she harbors no resentment toward the laguz - all because Daein's spineless Prince Pelleas told her to. It turns out, Pelleas has to obey the Senate, as he was tricked into signing a blood pact - basically a contract that would kill the citizens of Daein is its owner wills it. She explicitly states that she would gladly Jump Off The Slippery Slope if that's what it takes to keep Daein safe (thankfully it never comes to that).
FE10 plays with this trope with Jill and Zihark most especially; averted in FE9, played straight at the beginning of FE10, and then it depends on whether the player recruits them or not. It gets to the point where they're willing to betray their friends and principles just for their country, which is plainly in the wrong.
While not a soldier in any way, the character Nathaniel Vargas from Fallout 3 believes all the Enclave (former Éminence grise of the U.S. federal government) propaganda he hears and seems adverse to questioning the government in general if you talk to him about it. It can be entertaining to argue with him using examples from the U.S. Declaration of Independence and Bill of Rights; he'll eventually cut off the discussion for the explicit reason that you might convince him. Ultimately though, he may warn you, if still alive during The American Dream quest, to get away from the Enclave before they catch you, as he was taken captive by the Enclave and is in the Raven Rock base cells. His exact words: "They're not who they say they are... Get out while you can, before they get you too."
In Fallout: New Vegas, Veronica is loyal to the Brotherhood of Steel, despite believing that they will slowly die out if they don't change their isolationist and xenophobic ways. At the end of her personal quest, she'll either choose to stay with them or leave them, where she will see just how fanatical they can be when it comes to those with progressive thoughts. The current Elder, Nolan McNamara, has similar beliefs, but is hindered by his fear of the NCR and an unwillingness to go against tradition and commit outright heresy.
Similarly, we have Craig Boone, a former NCR 1st Recon sniper. Despite his disagreement with certain actions, like the Bitter Springs massacre, he is still a strong supporter of them, and will outright refuse to come with you if you get on their bad side, though as long as you avoid doing so he has no problems with you siding with House or going Wild Card (though it helps that both of those involve opposing Caesar's Legion).
Rose of Sharon Cassidy or "Cass" has similar sentiments, and provides the page quote. She's an NCR citizen and proud of it, but she realizes that the NCR is an overextended bureaucracy that just can't help the people of the Mojave in their current state, even if they do mean well. She prefers the Courier to side with the NCR for the game's central conflict, but doesn't mind the Courier being the Wild Card, mostly out of loyalty to them (Though it's implied that she's secretly horrified at the Courier for defeating three armies at once).
Despite trying to invade half a dozen countries at once to expand its borders and avoid an economic crisis, Belka in Ace Combat Zero had corps of extremely loyal pilots proud of their own nation. In an interesting game concept, there are cutscenes of interviews of the Belkan pilots the player fought, depicting them as obviously likable men ten years after the war.
Probably helped by how Belka detonated 7 nuclear weapons on their own country late in the war. But the pilots explicitly state that they hold no animosity towards their enemies, during and after the war. It was just war, and it was just what they were trained to do. In fact, many of them revere Cipher, the player character, in a decidedly odd twist. One character even states that Cipher is comparable to the old orders of Belkan Knights, an honor that he doesn't even give himself.
And Ace Combat 5 provides a subversion in that one of the Belkan pilots (one of their top aces in fact) takes an opportunity to defect after said nuclear explosions.
Actually he defected prior to it, as he would have been one of the pilots tasked with carrying out the strike mission. Killing millions of your countries citizens, and thousands of soldiers from both sides, will make you question your boss, that for sure.
Yellow squadron and Strigon team also have shades of this.
This is why General Leo of Final Fantasy VI is a Worthy Opponent rather than on your side. Even when he turns on Kefka, he's just trying to remove a piece of rot from the good name of The Empire, resulting in an awesomely tragic Heroic BSOD when Kefka reveals that he's acting on the orders of the Emperor, and Leo's fate is sealed by his inherent goodness. Poor bastard.
In the beginning of Final Fantasy IV, Cecil (the main protagonist) is the same as Leo above. After a particularly horrible mission given by his king, he becomes The Atoner instead, kickstarting the plot.
General Morgahn in Guild Wars. He is shown from the beginning to be an honorable officer who is also a loyal subordinate and friend of Varesh Ossa (for instance, he defends the Warmarshal at the joint tribunal following the mission in which the player discovers conclusive evidence of Varesh's villainy), though, as the Nightfall campaign proceeds, he expresses increasing concerns and doubts about Varesh's actions and finally defects to the player's side after Varesh's Moral Event Horizon crossing - massacring the priests of his patron goddess, Lyssa.
Harpuia of Mega Man Zero is a good example. A good character (or neutral at worst) in a Lawful Evil government, He legitimately seeks to protect humans. Too bad the definition of Maverick has become distorted.
The Suikoden series does this a lot, essentially, in every game, in accordance with its shades of grey approach to war. In five proper games and several side games/spinoffs, there are less than a half dozen truly evil antagonists and more than a few instances of What the Hell, Hero? moments from your own side.
Teo McDohl from the first Suikoden. However, he sends his two right hand men to fight for his son against his emperor.
A number of the generals are this until you beat some sense into them. Many of them still profess loyalty to the emperor even as they join you, but find themselves in opposition to the country's direction under Windy. Most of them rejoin the reformed government.
In II, Culgan and Seed.
Jowy loves his country and would rather reform it by taking out Luca Blight using Xanatos Speed Chess than see it ravaged by war thanks to the disjointed alliance that is the city states.
The Zexen Knights in III open the game as this as they, Chris in particular, are opposed to the Zexen council's motives. This leads to a bit of The Atoner with Chris (and Salome removes the corrupt councilmen).
Sasarai in III is this. He's not all that elated with seeking out the True Runes in the grasslands, but follows through until the issue becomes much larger. Then he finds out that he is an Artificial Human cloned from the dear leader as a placeholder for a true rune. Despite this, he still goes back to his position once the war is over.
IV has Troy. Given the trend of the games to have these types of characters eventually come around in the end, many fans were disappointed in the lack of a Heel-Face Turn, given that he was one of the few interesting characters in the game.
In V, there is a distinct divide on the Queen's nights concerning the Godwin rule. While some of the knights are quick to align with the prince, some align with the Godwins, and another considers his duty to Queen and country rather than any faction.
General Forsythe in Advance Wars: Days of Ruin fights only for the glory of his country, treats commanding officers and soldiers in the New Rubinelle Army with honor and dignity, and refuses to use Caulder's doomsday weapons to take them out. In the one mission where you go toe-to-toe with Forsythe, he actually comes and gives you advice on how to beat him. His AI is not aggressive, as he usually tries to beat you by blocking factories and sending infantries straight to your HQ. When you do beat Forsythe, he surrenders without a fight, on the sole condition that his army is treated with dignity, and he takes all the blame that his comrades deserve. Honestly, considering that the player is fighting under Admiral Greyfield's banner, it could be argued that you're on the "bad" side at that point in the game.
In dialogue, it's implied that Greyfield was the aggressor, and explicitly stated that Forsythe was called out of retirement to defend Lazuria.
Can be utilized by both the antagonists and protagonists in Ogre Battle: March of the Black Queen. A good amount of the enemy generals feel this way, and if you're enough of a dick or just plain unlucky (damn you tarots to hell!), yours begin to think this way as well. Except forDeneb.
Sam Carter from Deus Ex. He remains loyal to UNATCO even after it is revealed that the organization is just a front for Majestic Twelve. As he puts it, "We've got our share of crooked bureaucrats — fact — but this is still UNATCO, and by and large the people in this building are twenty-four carat gold." He does eventually join you against the Big Bad anyway, but only after UNATCO kicks him out, because they don't think he's loyal enough (or rather, not blindly loyal and able to recognise UNATCO's faults, which is what they don't want).
In Warship Gunner 2, Admiral Amagi of the Imperial Japanese Navy initially aids the player character because Japan is an ally of your nation, but later becomes a recurring enemy when Japan aligns with The Empire. So does Captain Tsukuba if he doesn't become your adjutant.
Nords loyal to the remains of the Empire in The Elder Scrolls V: Skyrim display some of this: they're dealing with a civil war where the other side is led by a secessionist whose grievances against the Emprire are genuine in spite of his "Skyrim for the Nords!" beliefs and many will adknowledge that the Nords have got a raw deal from them - scores of them killed in a war the Empire lost to the Thalamor, worship of their favorite deity, Talos, outlawed as part of the peace treaty, and heavy taxation to pay the war debts wrecking the economy. But as the first Imperial loyalist you could befriend in the game states, Skyim has always supported the Empire (Talos/Tiber Septim the first Emperor was a Nord) and "The Nords have never been fair-weather friends."
Metal Gear Solid: Peace Walker gives us even more backstory for her, and we find that for decades before her final sacrifice for her country, the government she served had been scapegoating her, manipulating her and treating her with enormous ingratitude, and that she allowed it - even encouraged it - because she was just that loyal. In fact, the only reason she got into the position to make the sacrifice possible in the first place is that other people constantly screwed up and wouldn't own up to their mistakes, and she allowed herself to take the fall for it all because that was the best thing for her country.Damn.
Jonathan's attitude towards the Eastern Kingdom of Mikado in Shin Megami Tensei IV. He rationalizes his actions as a Samurai as for the betterment of his country and optimistically believes the best of the current rulers, while choosing to turn a blind eye to the social problems that threaten to destroy it.
General Shiva from Exo Squad. Despite all the atrocities that Phaeton or the other generals, Draconis or Typhonus, commit, he stays loyal to the Neo Sapien regime since he is a soldier. It becomes a Tear Jerker when he dies in his final battle, which seemed to be used since he had outlived his usefulness to Phaeton, who was already phasing out the Neo Sapiens with the Neo Lords.
What seems to be going on (due largely to extremely intense propaganda starting in elementary education) with a large portion of the Fire Nation military in Avatar The Last Airbender, since while they get a lot of use as Faceless Mooks and the pacifist kid heroes are killing them before the end of season one, we also get brief characterization. Jeong Jeong's band of deserters decided that the wrong was too wrong and scarpered, and Zuko eventually decides to operate the "to be set right" part.
Iroh, significantly, appears to have decided this and then waited passively for five years for the right opportunity; before this he seems to have been a poster child for this trope.