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In stories which involve the military, relations between military officers and the politicians whom they answer to can often be a good source of dramatic tension. In some stories, it's the trigger-happy military which is the problem, but if the protagonists are military officers, it's a fair bet that the civilian side of government will either be ignored or will be presented as an obstacle.
It's not just the bureaucrats who are obstructive - it's the entire non-military world. All politicians, regardless of affiliation, are dedicated to blocking, budget-cutting, and otherwise screwing over the military for the sake of short term political gain. (And the criticism isn't just of pacifists - all politics is portrayed as inherently ignoble. If it's only politicians of a certain type who get this treatment, it might be a case of Strawman Political instead.) Courts and lawyers tie the military up with silly regulations which stop them doing their jobs. The news media never understand the realities of war, and reporters are critical of everything the military does. Businessmen just want to profit from the war, and don't care if their products are defective and get soldiers killed. The general public are ungrateful for the sacrifices made by the military. Even non-combat military personnel can be part of it, if they're fastidious about rules or are Armchair Military. Any character who isn't a soldier, really, has no plot purpose except to get in the way of the brave, noble, and self-sacrificing characters who are.
Because the author gets to determine how their world works, it's rare that the civilians will actually have a valid point. Even if they do, though, Sympathetic POV means that we may not notice it - since soldiers are the protagonists, we'll likely side with them without thinking too closely about whether it's really a good thing for the military to hold civilian authorities in contempt. A military protagonist in a You Have to Believe Me situation, say, may well look like a General Ripper from the point of view of the civilian, but since the audience knows better, the civilian appears to be unreasonable.
- Super Dimension Fortress Macross tends to present the military in a more favorable light than civilians, since the majority of the main characters are officers.
- It helps that the major civillian character outside of Minmay happens to be a gigantic douche. Also, the higher-ups in the UN Spacy (Adm. Hayase, for one) are shown to be a bunch of twits who are more interested in keeping up appearances for political reasons themselves. Really, in this case it's almost a case of Straw Anyone Who Is Not A Macross Crew member.
- Gundam Wing overlaps this with Your Terrorists Are Our Freedom Fighters. On the one hand, the protagonists (the Gundam pilots) are fighting against the corrupt Earth government oppressing the space colonies. On the other hand, people (on both the space colonies and Earth) are getting sick of the fighting. Which makes for lots of Contemplate Our Navels on the issue of war and peace.
- Unbuilt but visible in The Thing from Another World, where the scientists (especially Dr. Carrington) butt heads with the military men about how to deal with the creature.
- Inverted in Evolution, where it's the usual Straw Civilians that save the day from the Alien Invasion instead of the arrogant, pigheaded General Ripper.
- Tom Clancy's novels have this on occasion, though one line about people complaining about loud jets flying between bases was lightly mocked by a pilot for not liking "the sound of freedom".
- Clancy averts this trope as often as he plays it straight, however. Generally, whilst civilians often get in the military's way, their plight/position is portrayed with respect - in The Cardinal of the Kremlin, for instance, the President's Chief of Staff argues against rescuing the titular American spy, citing the fact that it could compromise dramatic diplomatic successes. Whilst the protagonists are against him, his argument is given a fair hearing.
- BattleTech fiction leans heavily towards this. The less military experience the ruler of a Successor State has, the less trustworthy they are. (The one exception to this rule may be the late Melissa Steiner-Davion, and even she had to pick up a gun and get her hands personally dirty at a young age when kidnappers came calling during one interstellar voyage.)
- People in The Sword of Truth are supposed to look foolish for not joining Richard's empire and disagreeing with his strategy of total war against the Imperial Order. But look at it like this. Richard is descended from the line of the Rahls, notorious for being crazy power hungry bastards. He ascended to rule the D'Haran Empire by killing his father. He continues to employ the Mord-Sith, whose primary purpose for existing is to torture people. Most of the claims about the Imperial Order's evil initially comes from Richard and his own soldiers. And he's continuing his father's expansionist policies, and also insisting that people perform the devotion, in which they spend a total of four hours every day essentially praying to Richard. (There's a magical reason why this protects them, but most people don't know about it). He's also fond of making references to how much killing he does. Oh, and he broke a little girl's jaw. Would you trust this guy? Well you should, because he's right, and if you don't join with him the Order will kill and rape everyone in the country. Although that may happen anyway.
- A surprising aversion is the Romance of the Three Kingdoms. Despite the fact that the military officers are usually portrayed well, there are several times where it is shown that they are wrong in not wanting to bow to civilian authorities. Good examples include Guan Yu and Zhang Fei's resentment of Zhuge Liang before his plans win the day at Bowang Slope and the Wu military's resentment of Lu Xun before he shows his worth at Yiling.
- Not so surprising, when you consider that traditionnal chinese wisdom despise military career to the benefit to civilian bureaucratic service.
- In Starship Troopers, pretty much anyone not willing to pick up a rifle and stand a post is treated like this, regardless of their actual reasons for not serving. In addition, civilians are portrayed as being incapable of really understanding the need for a military at all.
- Edge of Apocalypse takes this Up to Eleven, with the protagonist being a private contractor who designed a missile-defense system that works by reprogramming missiles via a laser to send them back to their point of origin. He consistently refuses to let the American Congress even see the details about the system they're paying for, because he feels only he can be trusted with it. In this story, he's completely right because all the politicians who want information about the system that will essentially nuke any location a missile is fired upon, whether the President or anyone wants to do so or not, are working with foreign conspirators who want to bring the U.S. down into a One World Government. Unsurprisingly, it's from one of the co-authors of Left Behind.
- JAG: became more obvious when the producers were given official approval by the Pentagon. Strawman News Media characters were a common occurence. 
- Battlestar Galactica can wander this way. Given most of the characters are military figures or those who associate with them regularly, and that the Colonial Military of Galactica represents the only functioning organization they have left (such that fleet wide control, government and supply -including basics such as providing water - are impossible without them) this is hardly surprising. People who, often for good reasons, try to change things have to look bad to keep things steady, and it can veer too far on occasion.
- On the other hand the new BSG introduced the Adama/Roslin dynamic specifically to avert the way this trope appeared in the original series, given the tendency of the Council of 12 to always suggest some inane plan. For instance: The Cylons annihilated our civilization in a surprise attack during peace negotiations... so let's make peace with the Cylons and destroy our weapons to show we mean it this time! While the new series focusses more on the military, the civilian side hasn't been ignored.
- However, any civilian who wants to change the way things are run (Tom Zarek, Gauis Baltar) isn't really portrayed very positively, though there are other reasons (and more the former than the latter). In-universe, Colonel Tigh seems to think this way.
- Stargate SG-1 had the NID, a civilian agency that started out merely short-sightedly bureaucratic, but became full-blown villainous in no time at all. Furthermore, on almost every occasion where non-military groups learn about the Stargate, bad things happen; ranging from kidnappings, to assassinations, to creating brand new long-time villain characters. At least 2 recurring Goa'uld baddies were hosted by civilians who stumbled upon extra-terrestrial treasure troves.
- Plus it was at least partially their fault, as they suppress information about the Goa'uld which definitely made those situations more likely.
- The Stargate Universe also features the IOC (International Oversight Committee), a bunch of "obstructive bureaucrats". Sort of subverted in that both Richard Woolsey and Camille Wray end up being sympathetic characters.
- The outright power hungry tactics of Senator Kinsey and the NID overshadow what are in fact serious breaches of protocol and oversight in Stargate Command. We automatically take the side of SG-1 and the rest of the SGC because they are the protagonists, and the leaders of the team are by virtue of character nature not going to play it by the book. When you stop and consider the Fridge Logic of just how reckless SG-1 can be, you really start to sympathize with Richard Woolsey's interference with the program.
- Note that, as well-meaning as Woolsey was, one of his blunders resulted in a near-ascended villain getting free and rampaging through the SGC, killing indiscriminately. This actually becomes a plot point later on in the show: when Woolsey decided to have an Ori-corrupted Daniel (actually a part of Daniel's plan) put out of commission at any cost, Daniel specifically states that he didn't blame him and cited the previous incident as Woolsey trying not to make the same mistake again. The general theme seems to be that neither the military nor the civilians are entirely evil: there are just some corrupted individuals in both camps (Maybourne and Makepeace in the military, the NID amongst the civilians). Both sides have sympathetic characters who make mistakes.
- E-Ring had its share of both Straw Civilian and Military Obstructive Bureaucrats hindering or downright forbidding the Mission of the Week.
- Dr. Franklin fills this role in Babylon 5: He shunned military service (partially because of his father the general. He refused to help in creating bioweapons to fight the genocidal Minbari. He also constantly criticizes the other, more trigger-happy human protagonists. But then again, as the titular station's doctor he's the one who has to clean up after a firefight.
- And he was a junkie -- interpret it as you wish.
- Star Trek had a couple of these, most notably Nilz Barris from The Trouble With Tribbles.
- Kirk actually says that Nilz Barris is the first Federation official he has met whose competence he has questioned. That said, there were a lot of egomaniacal ambassadors and scientists who were consistently willing to put their own careers ahead of the lives of the crew. Though, the admiralty is usually depicted as being even worse.
- The show Parks and Recreation is actually told from the perspective of bureaucrats. Whenever the main characters interact with the public, the members of the public are portrayed as a collection of weirdos and morons. For example, one public forum featured a woman complaining to the Parks Department because she found a sandwich in one of their parks and was upset that it didn't contain mayonnaise.
- And then there was the episode where a man chained himself to the protagonist's desk and refused to leave until she agreed to put a copy of Twilight in the town's time capsule.
- From the famous "St. Crispin's Day" speech in Henry V we have the following lines, disparaging those who would not fight with Harry at Agincourt.
And gentlemen in England now a-bed/ Shall think themselves accursed they were not here, And hold their manhoods cheap whiles any speaks/ That fought with us upon Saint Crispin's day.
- Anybody who's non-military in the Gears of War series is shown to be a complete asshole to COG soldiers, though to be fair the military had to wipe out most civilian cities to deny enemy resources when things got really bad but they really had no other choice.
- Two words: Escort Mission.
- Duke Nukem Forever cheerfully plays this straight: the US President is an Obstructive Bureaucrat who outright states he should have ordered the CIA to assassinate Duke, while the Big Good of the game is General Graves, despite being mostly a Desk Jockey.