The word "terrorist" doesn't have a single, universally-accepted definition. The most commonly accepted definition is "a person who uses violence to achieve a political end." The problem is this: people who engage in a guerrilla war against an oppressive government can also be described as using violence to achieve political ends. It gets even worse if you define "violence" as the exertion of unwanted power - whether physical or psychological (which is the much broader original definition) - over an opponent, meaning that, technically, protesters employing passive resistance would also be "terrorists." Of course, as one term (terrorism) represents a modus operandi and the other (freedom fighting) represents a goal, there is no reason apart from optics why the terms would be mutually exclusive.
Another definition of terrorist is "one who uses terror as a means to achieve a goal." The problem with that definition is that it includes things like any policeman who uses the fear of getting shot to force a suspect to surrender, or your Wounded Gazelle Gambit-loving little sister.
Yet another definition is "one who commits terrorism," itself defined as "the use of terror tactics to bring about social or political change." This is better, but still problematic given that much of warfare has always been about destroying your opponent's will to fight.
To add one more definition to the already-muddled pot, the UN defines terrorism as attempting to bring about change by deliberately targeting non-combatants. This is compared to legitimate warfare, where soldiers are at least supposedto only attack military targets. Or in plain English, it's not what you're doing that makes you a terrorist, but who you're trying to do it to. This line becomes blurry when "collateral damage" is taken into account (see also Nice Job Breaking It, Hero).
The ragtag band of plucky rebels fighting against the evil Empire will see themselves as "freedom fighters," although it looks a lot like "terrorism" to the guys they are against.
There is basically no definition for "terrorist" that could not fit most modern state actions in some manner, except maybeStephanie Miller's ("Ideologically-driven organized crime"). Maybe.
See also You Rebel Scum! Tends to happen when dealing with a Villain with Good Publicity and/or a Hero with Bad Publicity. Related to Well Intentioned Extremists and is a subtrope of La Résistance. Likely to overlap with The Revolution Will Not Be Civilized. May result in Moral Myopia if the supporters of La Résistance accept and excuse actions from La Résistance that they condemn The Empire for doing. Which label gets applied long after the fact will most likely depend on which side won and how.
Implicit in most politically correct discussions of terrorism and fictional uses of this trope (including much of this page) are: 1) a near-exclusive focus on the concrete tactics used by each side, 2) an equating of (or a refusal to judge) the actual fundamental goals of each side, and 3) an acceptance of moral subjectivism.
This happens in multiple Gundam series, such as the AEUG and Karaba of Zeta Gundam, and the League Militaire of Victory Gundam.
Gundam 00's first season averts this, as Celestial Being don't claim to be La Résistance. Season 2, however, has Celestial Being allied with Katharon, a Karaba-Expy organization who fit the trope better.
Gundam Wing's five protagonists of Operation: Meteor were sent by Colonists against the oppresive Oz of Earth. Many of their attacks felt like terrorist movements, until we learned what they were targeting was in fact very specific. Granted some collateral damage.
In Ghost in the Shell: Stand Alone Complex, the third and fourth World Wars have left Japan with a large population of refugees (probably Chinese and Korean), who live in camps made of ruined and abandoned cities enclosed by fences and guarded by the military. Forced to live in poverty and without any place to go, many of them resolve to take hostages, assassinate political officials, and perform suicide bombings to force the government to give them a new home. In the second season, one of the two main antagonists is a Japanese man who becomes one of the rebels' greatest leaders and is considered a hero for the refugees, but the country's top terrorist by the government. Given that Ghost in the Shell deals heavily with conspiracies, things are a lot more complicated, though.
Then there are the Individual Eleven who claim to represent the will of the mainstream Japanese populace, and pursue "refugee liberation" (read: "kick them out of the country!"), who also commit terrorist acts in the name of their cause. In the first episode of the second season the Major in turn compares the Section 9 to a terrorist organization, since they're a secret armed group that lacks governmental recognition or supervision - they do get the said recognition later in the same episode, though.
The title characters of Nanatsu No Taizai are considered as criminals before and after they were framed. However a number of them are good people at heart. When a princess decides to seek them out to save her kingdom, they become this trope.
One Piece plays with this concept a bit. The main characters are pirates who don't do pirate like things, instead taking out other pirates and corrupt organizations/local governments, but this hasn't stopped them from being labeled as highly dangerous pirates by the world government (it doesn't help that some enjoy being called pirates) and heavily feared by most citizens, although the citizens they've helped out seem really grateful and forever in their debt. The fact that a few of them were already on the run from the world government for political reasons (they knew something the world government didn't want the public to know) and the organizations had major ties to the world government, which is possible just as corrupt as the others they've encountered and employs some monsters in their "fight against evil" doesn't change the fact that the average citizen fears the worst from them and not the world government and theirs.
In the Area 88 manga, Mickey meets Rishar Vashtal, Saki's brother and a leader among Asran's anti-government forces. Rishar explains the anti-government forces' reasons for engaging in the civil war, showing that both sides of the conflict have legitimate aims. Mickey feels conflicted after meeting Rishar but remains loyal to Area 88.
Mickey: I didn't want to hear his problems. It'll be harder for me to fight now.
In RideBack, The GGF (or GGP, as in the anime) shows fractures after overcoming superpower forces as terrorists themselves, becoming a believed-benevolent world military enforcer. A splinter group of GGP ex-pats becomes a terrorist force against their old comrades.
Buffy the Vampire Slayer: The basic view of the world in Season 9, with Slayers being seen as terrorists persecuting vampires who are now beloved. Simone does not help, her appearance in the first issue even invoking that she is a domestic terrorist.
In DMZ, the terms terrorist and insurgent get thrown around pretty casually, and are frequently directed to innocent bystanders who just want to get on with their lives without taking either side in the USA's second civil war. Naturally this also happens in a more textbook fashion with regards to the rebelling faction of said Civil War.
Freedom Fighters uses this as a recurring theme with the team usually viewed in a negative light. Their earliest stories featured them as the only heroes on a world controlled underneath Nazi rule, which makes this trope very obvious. More recently they are antagonists of the black-ops government organization S.H.A.D.E. which leads to Uncle Sam, the living embodiment and spirit of the United States, being declared a threat to national security and put on their most wanted list.
This is a prominent theme in Savage, with the title character considered a heroic freedom fighter by the British, but a brutal terrorist by the occupying Volgans.
In the Buffy the Vampire Slayer / Star Trek: The Next Generation crossover story "Legend", Buffy is rescued from cryogenic sleep by the crew of the Enterprise, who view her as an early 21st Century terrorist leader and a war criminal because of Buffy's activities during the Eugenics Wars. Of course, what she was really doing was rebelling against Khan Noonian Singh, but you know what they say about who writes the history books.
The Conversion Bureau stories explore this with both the Human Liberation Front (HLF) and Ponification for Earth's Rebirth (PER):
The PER: Saviors of a fallen humanity? Or Quislings who've thrown away their humanity in exchange for "paradise"? Or Knight Templars who believe everyone should be ponified — regardless if they like it or not?
In Dauntless, the various groups opposing Brittanian occupation of Japan run the gamut. Lelouch adjusts his methods of dealing with them accordingly.
The small resistance force whose members include Kallen, Ohgi, Tamaki, and the late Naoto is also the most idealistic one. Lelouch is perfectly willing to grant them amnesty, providing they don't cause any more trouble since he wants to recruit Kallen.
The JLF are also pretty idealistic and honorable, though they are willing to do harsher things for their cause. Lelouch is willing to let them go into exile in China since he wants to use them at a later date. He makes an exception for the JLF member who ordered an attack on civilians, including Lelouch's former schoolmates and sister Euphemia. Lelouch considers that man to be nothing more than a cowardly terrorist, and he demands the man's head.
The Kenshiki Faction is the worst of the lot. A group of zealots led by a foreigner hating bigot and an Entitled Bastard who are willing to kill hundreds of civilians, even their fellow Japanese, to get their way. They attack a hospital and kill everyone inside as a distraction for an assassination attempt on Lelouch, and they later blow up a school just to get at Euphemia. The above resistance groups abhor their methods — Kallen is enraged by what the Kenshiki did to her school and the JLF refuse to take the pragmatic route of coordinating their attacks with the Kenshiki's in a pincer move since they don't want to be associated with the Kenshiki. Even an arms dealer hates them. Lelouch classifies the Kenshiki as terrorists that must be exterminated with extreme prejudice.
In Prison Island Break, Sonic the Hedgehog thinks of himself as a freedom fighter. He's the mascot of some sort of party that's opposing the current government and he's in prison for it. The author hasn't even clarified whether the government Sonic opposes is a democracy or not, and has suggested that his party should be thought of in terms of the IRA.
In Sailor Moon canon, the Black Moon Clan and their ancestors were terrorists who invaded Crystal Tokyo and destroyed it. In ''I'm Here To Help, the group is portrayed as a bunch of noble freedom fighters trying to overthrow a corrupt government. Given that the narrator of the fic is the last living and free member of the group who is pretty clearly insane, it's difficult to say which interpretation is more accurate. That survive is alluded to invoking a number of questionably moral actions himself, including destroying buildings and causing the deaths of civilians, which he claims is done in the name of trying to save said civilians.
In V for Vendetta, V is labeled a terrorist by the fascistic government of Great Britain he is trying to overthrow, and even calls himself a terrorist in the original comic. The question the comic is asking is essentially "is a good cause corrupted when reprehensible methods are used to achieve it?" Even the author, Alan Moore, a outspoken proponent of anarchy, says that the anarchistic V is not supposed to be a clear cut, definite hero, and Moore's main issue with the movie was that the film painted V as unquestionably being a freedom fighter and the hero of the story.
The Rebel Alliance in Star Wars. Debates on its morality and the innocents have cropped up everywhere, most memorably Clerks and the question of independent contractors killed on the Death Star.
In the Expanded Universe novel Sacrifice, Luke Skywalker's own son acknowledges a lot of innocent people died when the Death Star(s) exploded. Luke himself noted that it had more than a million people on board, not counting the droids. Let's not even go into the prisoners being held on that battle station when it blew (Leia was a prisoner there, and Luke and Han had Chewbacca pose as a prisoner).
There's also Star Wars: TIE Fighter, where you are a star fighter pilot in service to the Empire, which is presented as the guardian of order, and the Rebels are portrayed as terrorists (though Vader still scares everyone and you don't actually fight Rebels that much). In fact, most of the early missions consist of legitimate work like scanning freighters for contraband and defending military installations from attack. The Opening Scroll and cutscene in TIE Fighter specifically refer to "Rebel terrorists" and "Rebel insurgents."
All of the Star Wars flight sims, and their companion comics and novels, play with this trope in regard to capital ship names. Those stories told from the Rebel perspective are likely to include Alliance ships named after ideals - "Independence," "Liberty," "Freedom" - while enemy ships have names with definite negative connotations - "Inquisitor," for example, or even "Eviscerator." If, however, the protagonists fly for the Empire, suddenly all the Star Destroyers have names like "Protector" or "Stalwart", while the ships of their Rebel opponents have non-evocative names.
The Zionite Rebels in The Matrix are active terrorists who go so far as to advise new recruits that every living human still within the Matrix is a potential enemy, since the bad guys could teleport in by taking over the bodies of any still living bystanders, despite the fact that they are nominally fighting for the exclusive benefit of these humans.
The Matrix Online took this idea and ran with it, establishing the new conflict as solely for control of the Matrix, because everyone needs it. Morpheus was unwilling to admit it and staged terrorist attacks with the end goal of crashing the entire thing; he was left to do it largely alone, with even Zion distancing itself from him.
The Beast Of War from the same year has a similar plot, though slightly more realistic. "Sorry, sir. Not much of a war. No Stalingrad. How is it that we're the Nazis this time? How is it? I tried to be a good soldier. But you can't be a good soldier in a rotten war, sir."
In Steven Soderbergh's two-part series about the real life Ernesto "Che" Guevara, Che (played by Benicio del Toro) is a mostly shown as a freedom fighter in Part 1. In Part 2, his revolutionary movement doesn't catch on and he's seen as a terrorist.
Defied in Die Another Day. When Bond is told one man's terrorist is another man's freedom fighter, he states 'Zao (the man he's hunting) has no interest in other people's freedom.'
In National Treasure, Benjamin Gates, when at a gala in the nation's capitol, makes a toast to treason, pointing out that that's what all the founding fathers would have been charged with if the Revolution had failed.
Some people call me a terrorist... I consider myself a teacher.
Discussed in Muppet Treasure Island by Long John Silver during the "I Am" Song "Professional Pirate," who notes that whether a pirate is considered a hero or villain depends on who tells the tale, offering the English and the Spanish's differing opinions on Sir Francis Drake.
Captain America: The Winter Soldier has this as the main plot as Cap is framed for supposedly killing Nick Fury and branded a criminal as such. It became quite literal at the end when it's found out the HYDRA is behind everything and manipulating events from within S.H.I.E.L.D so they can take over the world.
Animorphs: A major theme of the books, with many an anvil dropped.
Good Omens contains this exchange, between an angel and a demon:
"Maybe some terrorist—?" Aziraphale began. "Not one of ours," said Crowley. "Or ours," said Aziraphale. "Although ours are freedom fighters, of course."
To further drive the point home, when they compare their respective lists of terrorists/freedom fighters in their employ, half of them turn out to 'work' for both sides.
The Discworld Companion, also by Terry Pratchett, notes that the subtle distinction between gods and demons on the Discworld is 'like that between terrorists and freedom fighters'.
The Varden in the Inheritance Cycle are a very good example of this trope. They make it very clear they consider themselves freedom fighters, and the empire as harmful, but the Empire's supporters (and pre -villainisation Murtagh) occasionally call them out for their less than stellar behaviour, so obviously some people think of them as terrorists.
The non-fiction work Going Nucular discusses politics in language, and pretty much shows how this trope is Newer Than They Think. The author notes how just as the French Revolution's government called themselves the "Reign of Terror" in the sense of being a "holy terror" that defeated their evil enemies, lots of resistance groups of the Bomb-Throwing Anarchists type were quite happy to call themselves terrorists, since it didn't carry the implication of being the bad guys. Pretty much the last to self-identify as terrorist were the Irgun in Israel's war of independence.
Interesting variation: Elphaba in Wickedis a terrorist. The word never comes up, but the issue is similar. Your Wicked Witches Are Our Freedom Fighters?
Winds of the Forelands brings up the issue in that the lower-ranking rebels consider themselves freedom fighters. Their leader is genocidal, so the counterinsurgents can keep A Lighter Shade Of Gray and avoid having to address the Fantastic Racism that led to the rebellion.
The thin line between special operations and terrorism is a key theme of Shadows of Steel.
In Warrior Class, the Turkish general visiting Nellis AFB denounces Kurds as evildoers, to which American Colonel Rebecca Furness notes that the American public would find (public knowledge of) bombing Kurds distasteful. Not too much later, the German and Russian foreign ministers discuss how Muslim "terrorists" creating havoc for both their peoples, who aren't squeaky clean themselves, are abetted by American funding.
The Audubon Ballroom in Honor Harrington is the galaxy's most notorious band of terrorists, or freedom fighters, depending on how you feel about the Manpower Corporation, and genetic slavery.
And of course, there are few things as brutally violent as Havenite grassroots political movements. Eventually it becomes apparent that the leading cause of death in Nouveu Paris is having an interest in politics.
Several other examples begin to pop up in the later books.
In Alexander Yang's Midnight World series Vampire Hunters are branded as terrorists - because the world is ruled by vampires.
In Blacklisted by Gena Showalter, this trope is explored with drugs. It's more like "Your Illegal Drug Dealers are our Pharmacists". In a future America, aliens are commonplace, but most of them have to take a drug to breathe. This drug, however, is illegal. The main character's love interest sells them, and is hunted by the government.
Twenty Thousand Leagues Under the Sea: Captain Nemo is an early example: he adopts the Ocean as his new homeland and finances the Cretan rebellion because he hates despots. However, the Nautilus permits him destroy any of The Empire’s ships with total impunity (no Nation could chase him in the bottom of the sea). His superior technology means that even the military is as helpless as ordinary civilians.
In The Tomorrow Series, Ellie and her friends are considered terrorists by the enemy...and in a lot of ways, like not wearing uniforms or having a clear chain-of-command, they do fit the bill remarkably well.
In the later chapters of The Poisonwood Bible, this frequently comes up in arguments between the pro-colonialist Rachel, and her sister Leah, who is married to a (mostly non-violent) freedom fighter.
Forever Gate: The Users are known as terrorists becuase they advocate for a collar-free society. Their leader is proud of the fact that they've never killed a single human in their activities, which include leaving bombs in public areas.
The issue is directly referenced by name in Season One, during the election dispute between Laura Roslin and Tom Zarek, a notable radical who had served twenty years in prison for blowing up a building during an insurgency on Sagittaron before the war, and thus is regarded in legal terms as a terrorist. A Roslin supporter sitting at a bar makes a comment regarding Tom Zarek as a terrorist only to have a Tom Zarek supporter sitting nearby immediately correct the man that Tom Zarek is a freedom fighter. The argument soon evolves into a brawl, but this view is shared by Zarek's supporters as well as Zarek himself, and his ability to market himself as a heroic, populist figure sways nearly half of the fleet (though Dualla, who's also from Sagittaron, is disgusted by the support he gets, feeling there's no justification for what he did, not even their world's freedom).
In Season 3 during the Cylon occupation of New Caprica, Colonel Tigh flatly states "Which side are we on? We're on the side of the demons, Chief. We're evil men in the gardens of paradise, sent by the forces of death to spread devastation and destruction wherever we go. I'm surprised you didn't know that." when confronted by Chief Tyrol over the use of suicide bombers and terrorism against the Cylons and the humans who work for them. Although, he could just be being sarcastic after Tyrol expresses outrage over the use of suicide bombers against the Cylons (who can resurrect), which Tigh seems to justify under I Did What I Had to Do.
Continuum: The villains belong to Liber8, a blood-thirsty terrorist group who have no qualms about killing innocent people to achieve their political goals... which just so happen to be overthrowing an oppressive dictatorship in order to restore the Bill of Rights to a corporate-controlled America. Seriously... these murderous thugs are perfectly willing to slaughter thousands of people in a bombing if it means that Freedom is returned to the people. And remember... the hero of this story, Kiera Cameron, is trying to stop these rampaging Democracy-advocating, freedom-loving, liberal-minded monsters.
Heroes: In the episode "Five Years Gone", Hiro and Ando are shocked to find that Future Hiro has been labeled a terrorist by the government.
Leverage: In one episode, a group of militiamen claim to be 'anti-government freedom fighters', which gives them the right to kill two IRS agents as enemy combatants. Later they are revealed to be making a bomb to blow up a civilian target.
Elliot: "See that's the difference between a real soldier and this little hallowe'en outfit you've got going on. You'd kill to protect your rights. A real soldier? He'd die protecting somebody else's."
JAG: The second season episode "Trinity", featuring the IRA, characterized them as rugged yet heroic freedom fighters, with the main characters aiding them for a while (in fairness it was to recover the infant child of a US service member stationed in the UK and an active IRA member based in Northern Ireland) and the episode amazingly goes so far as to portray a suicide bombing by an IRA man against the British as an Heroic Sacrifice. This episode was broadcast before the Good Friday Agreement when The Troubles were still ongoing. It naturally thus goes out of its way to demonize the main RUC detective as a Dirty Cop, or even worse.... However, the episode did not portray the British as evil per se, as one exchange between Harm and Mac near the back at Heathrow Airport suggests that the British authorities will deal with the Dirty Cop.
Mac: The Brits picked up Hutchinson in Londonderry. Have him on a suicide watch.
Harm: Well, they wanna make sure he gets to trial.
Merlin has the magic-users in a very good show of the trope. While they commit many crimes of terrorism, only a few of them are truly evil, the rest are just fighting for their right to exist. Even the ones that are were WellIntentionedExtremists long before they were villains.
Revolution: In episode 2, Monroe calls a rebel he's torturing a "terrorist". He has a point, because episode 5 had rebels Ken Hutchinson and Nora Clayton try to blow up a train with militia officers...and a civilian named Danny in it. Things broke down between the two when Nora tried to abort the attempt, and Ken insisted on continuing it, which resulted in him stabbing her non-fatally in the gut. Then again, the Monroe Republic did try to systematically exterminate all the rebels in episode 11, so the rebels definitely have freedom to fight for. Not to mention that the first season finale reveals in a flashback that a rebel bombed the restaurant Miles and Monroe were in, injuring Miles, and Monroe, acting on his borderline erotic fixation for Miles, murdered the rebel and his entire family in an ill-conceived attempt to make an example out of them.
The Sarah Connor Chronicles: When accused of acting like some kind of terrorist organization, Sarah flat out states "We are some kind of terrorist organization."
Stargate SG-1: In the episode "2010", the team's efforts to change the timeline into one where humanity doesn't go extinct is called a "terrorist attack".
The Bajoran freedom fighters in the backstory of Deep Space Nine used whatever means necessary to free their home planet from Cardassian rule, though it seems that suicide bombings were not standard procedure. The Cardassians (with some justification) prefer to call the Bajoran freedom fighters terrorists. Gul Dukat even called Major Kira a terrorist to her face... and she didn't deny it. Indeed, she's kinda proud of it. There's a point where Kira finds the Cardassian file on herself, and she's actually upset that they only looked at her personally as a minor nuisance. In "The Darkness And The Light", Kira outright screams her defense of terrorism (at least when it comes to Occupiers Out of Our Country) to a Cardassian who's taking revenge on members of her former resistance/terrorist cell, who maimed him in a bombing:
"None of you belonged on Bajor. It wasn't your world. For fifty years you raped our planet, and you killed our people. You lived on our land and you took the food out of our mouths, and I don't care whether you held a phaser in your hand or you ironed shirts for a living. You were all guilty andyou were all legitimate targets!" (This last was because he made a point of noting he'd only been a civilian worker, rather than a soldier, during the occupation on Bajor).
The same can be said of the Maquis and their tactics against the Cardassians.
The Cardassians themselves used terror tactics against the Dominion when the latter occupied the Cardassian homeworld. Kira even went to the Cardassians to teach them how to properly set up a terrorist cell. They actually called them that: terrorist cells. Yes, DS9 is a pre-9/11 show; why do you ask?
Star Trek: The Next Generation: The episode "The High Ground" dealt with the "you say terrorists, we say freedom fighters" issue. The Ansata separatists are trying to overthrow their Rutian oppressors "by any means necessary", including suicide bombers (while the government they're fighting makes use of indefinite detention, and in the past, simply killed people). During this episode, Data notes the "historical fact"note as decreed by Paramount, in contrast to the original script that Ireland was reunified in 2024 after a successful terrorist campaign (which is why this episode wasn't broadcast in its entirety in either Britain or the Republic of Ireland until years after.)
The Shield are entirely this, claiming that they attack other wrestlers who had done nothing to them, saying that they had done something they didn't like. But all we see them do is beat them up until they're no longer able to stand.
In 1776, Ben Franklin observes, "Treason is a charge invented by winners as an excuse for hanging the losers." This quote has been wrongly attributed to Franklin himself, but it was invented for the play (and later movie). Later, Dickinson characterizes New England as a hotbed of irrational, violent radicals.
John Adams: I have better things to do than sit around listening to you quote yourself.
Franklin opines on another occasion: "Rebellion is always legal in the first person, as in our rebellion! It is only in the third person, their rebellion, that it becomes illegal."
Epsilon of Mega Man X: Command Mission sees himself as the freedom fighter and a pioneer for Reploid evolution while the Maverick Hunters deem him a terrorist for his hostile takeover of Gigantis Island. Oh, and having a big missile for extra negotiating power too.
Tales of Phantasia actually mentions the trope almost word for word in some translations and adaptations! For those who don't know, Dhaos is only on Midgard to save his own people since his people need Mana to survive, while Midgardians don't. So the party and player views Dhaos as a terrorist and your group of five (or six) as the Freedom Fighters, yet by killing Dhaos, the party realizes that they doomed his people, making them the terrorists, while Dhaos was the Freedom Fighter. But it's implied Dhaos became a mana seed anyways.
In Command & Conquer 3: Tiberium Wars the Brotherhood of Nod, despite being the canonical bad guys, have achieved a status were they are the only hint of civilization, law and order in the war torn and ecologically collapsed yellow zones, where 80% of the world population lives, nevertheless, they are terrorists in the eyes of GDI, who happen to be the remaining 20% of the population, and have control over the pristine and wealthy blue zones.
Its even more messed up. Even in Tiberian Dawn, the Brotherhood has a slim majority of world support. Even in first world countries like the United States, they have a huge following (including sensitive entities like defense contractors) - they are the only bastion left to support your -isms that a one-world-order UN regime took away. Further complicated in that you often will see GDI killing innocents/civilians. In retrospect, it is easy to see why the majority of the world is Nod affiliated (but Nod has been known to kill civilians while disguised as GDI).
This trope also ended up biting Majestic 12 in the ass: they created the Daedalus AI with the purpose of cracking down on any group that could oppose their rule, which included all terrorist groups. Once the AI was switched on, it quickly came to the conclusion that Majestic 12 itself fit the definition of a terrorist group and turned against them.
PlanetSide gives us the New Conglomerate faction. Freedom is the NC's motto, but the Terran Republic (and possibly the Vanu Sovereignty too) view them as nothing more than rebels and terrorists. Due to Grey and Gray Morality, they're probably both.
A point passes in Chrono Trigger after which you cannot enter Guardia Castle in the year 1000 AD. Due to the corrupt Chancellor's actions, the government in that year classifies your party as "terrorists". The same party whose goal is to eliminate an evil extraterrestrial being whose presence dooms the world.
In Final Fantasy VII, Avalanche is labeled a terrorist group. They're the heroes. Not that hard to understand, as your first objective in the game is a bombing mission on a power reactor, with the group planning to bomb the others. Towards the end of the game, you even get called out on it.
Final Fantasy XII - Ghis: "No different than any mean member of the insurgence." Ashe: "The Resistance!"
Freelancer has The Order, which is first presented as a shady group of terrorists, then as a group of heroic freedom fighters.
Their whole purpose is to protect the Sirius sector from Nomad invasion and destruction.
In the Metal Gear series, Solid Snake and Otacon's Philanthropy is an illegal combatant organization at the very best, and it might have been a plain terrorist organization if they had let civilians appear in the game.
The titular Sons Of Liberty (MGS2) call themselves freedom fighters. They certainly are terrorists too. Same for FoxHound.
Philanthropy started as a UN organization; fringe though they may have been, they presumably kept that backing because Snake is very very good at what he does and it's not hard to imagine that their attacks were executed without any casualties. It is, after all, Snake being framed for sinking the USS Discovery and killing the US Marines on board that gets Philanthropy kicked to the curb by the UN and turns them into an illegal combatant organization, one that is ironically later backed by UN official Roy Campbell under the table. Snake never intended to destroy Metal Gear RAY in such an environment, the tanker mission was done solely to plaster evidence of its existence all over the Internet (of course, even if he did intend to do so, the only real affect it would have had on the environment is yet another sunken ship at the bottom of the harbor, as the Tanker in question was a fake tanker that didn't contain any crude).
On the other hand, Solid Snake himself does not deny that he is a terrorist as well, when Raiden pointed out that what he and Philanthropy is doing is more comparable to that than grassroots resistance, meaning they may have done some much less innocent stuff to get rid of Metal Gear in the past. Now, the Patriots are an interesting variation: Although they rule the country and are also implied to be the very essence of American ideology, they also frequently stage Terrorist attacks on their own soil and frame the "official" terrorist group for committing them. Metal Gear Solid 4 also implies that it was actually the Patriots who rammed Arsenal Gear onto Manhattan, presumably due to GW being corrupted.
The Renegades in Tales of Symphonia are a good example of La Résistance being made up of Well Intentioned Extremists - they start out the game by killing a bunch of innocent bystanders and attempting to kill the female lead to prevent her being used in the Big Bad's schemes. They consistently have their own goals and methods throughout the game; sometimes these goals coincide with the party's, and sometimes they're opposed.
Played with in Supreme Commander: In a three-side war between the militaristic UEF, religious Aeon, and anarchist Cybrans, everyone gets called "oppressors," "fanatics," and "terrorists." The strange thing is that this propaganda turns out to be true for the other two sides, while the one you pick is holding the Sanity Ball throughout. This goes as far as having the same characters be honorable and just when they're on your side, and psychopathic maniacs when they fight against you. For example, when you play for the Aeon, the Princess is genuinely concerned about enemy civilian population and instructs her commanders to avoid needless casualties, whereas in the UEF campaign she clearly tries to brainwash you and her commanders do the standard Evil Trash Talk about cleansing the entire galaxy of unbelievers.
The Anti-Nationalism Influence United faction in Ace Online is this to a T. For its supporters, it's the Last, Best Hope for Humanity Decaians, Philonites and Vatalluses. To the reigning Bygeniou City United, they're pesky terrorists. Both sides regularly commit Kick the Dog moments with one of the pre-set character avatars' history hinting to the ones done by the ANI faction.
In Starcraft, the player is rescued by and subsequently joins Mengsk's "Sons of Korhal," portrayed by the Confederacy as terrorists. In later missions, you will engage in what can only be described as acts of terrorism against your own kind, and Mengsk is eventually proven to be out to make himself Evil Overlord.
Later on in the storyline, Tassadar and Jim Raynor are portrayed this way by just about everyone else.
Taken to a literal degree in Freedom Fighters, where the eponymous freedom fighters are referred to as terrorist on the Soviet-controlled television network. Lamentably, in spite of this, Black and White Morality is in full effect in the course of the game itself.
The Freedom faction in S.T.A.L.K.E.R.. They fight for free access to the Zone (in all fairness, they only fight Duty, bandits, and the military, the latter two of which fight everyone), believing it could help advance humanity, while their rival faction, Duty, view them as a bunch of terrorists who want the Zone to expand.
Played straight in Tachyon: The Fringe, where whichever side you join treats the other as evil. GalSpan openly calls the Bora "terrorists," while the Bora consider themselves to be freedom fighters. Both are true. The Bora fight GalSpan for trying to kick them out of their homes, but they use guerilla tactics to achieve their goal. Of course, they are never shown openly attacking civilian targets, as opposed to GalSpan who blow up hospitals just to avoid a drop in stock prices.
The manual states that Bora started out as political dissidents who refused to accept the new One World Order after the end of the war in the Solar System and chose to leave through the first one-way mega-gate. Many years later, they are re-discovered in an area that is full of resource-rich asteroids. GalSpan invokes a Loophole Abuse by legaly purchasing the rights to Bora space from the Sol system government (because, apparently, Sol owns all of space), something the Bora (being dissidents) never bothered to do. It's no coincidence that the Bora campaign is the more difficult one while (in most players' opinion) being the morally right one.
Homefront follows your adventures as part of the resistance against the KPA (the armies of a United Korea). One of your men, Conners is just this side of Ax-Crazy but even he balks at the efforts of another group of resistance fighters who behave like the KKK.
In EVE Online, the Amarr use "terrorist" to characterize Minmatar who liberate slaves by force, or even simply attack Amarr military forces. The former definition includes a large section of the Minmatar roleplaying community, particularly the Ushra'Khan alliance. The latter includes virtually any player allied to the Republic, as well as the Republic Fleet itself. Needless to say, the Minmatar consider these same people to be freedom fighters, or simply soldiers.
The Witcher has the Scoia'tael, non-human guerilla brigades who attack human settlements and activities to protest racism, discrimination and having been made second class citizens. The Scoia'tael have very legitimate goals, ideals and grievances. However, their tendencies towards arson and looting, and perfect willingness to kill any human anywhere, anytime, have made them widely hated, even among the non-humans they are supposedly fighting for.
The Stormcloaks in Skyrim are considered murderous traitors and dissidents by some and heroes fighting for Nord freedom by others.
There's also the Forsworn, a group of Bretons who are native to the Reach. They see themselves as fighting for the independence of their ancestral homeland. Nearly everyone else tends to be a little less sympathetic given their tendencies for worshipping Hagravens, practicing necromancy and wearing the skins of their defeated opponents...
Many of the Daedra are considered "good" or "evil" alternatively by various people - for example, Azura for the former and Mehrunes Dagon for the latter. The main litmus test for whether or not a Daedra is evil seems to be whether their specific flavour of Blue and Orange Morality is compatible with the continued survival of human and elven civilisation.
Dragon Age II ends with party member Anders, a mage and a supporter of mage freedom from imprisonment by the Templars, blowing up the Kirkwall Chantry with its clerics and staff. While not explicitly moving against the mages, they are the ones who maintain the "peace" between the two— a peace which allows the Templars to hold on to their power while the mages continue to be abused and mistreated.
Arc The Lad: During the first two episodes, the Powers That Be are eager to present Arc and his companions as some sort of magically powered polytheistic Al Quaeda. Considering Arc and co.'s deeds during Arc 2 (blowing up landmarks built in the middle of densely populated metropolis with little regard for the collateral damages, blowing up religious buildings preaching against them, even slaughtering kidnapped orphans, some of them genocide survivors...) most people in the world believe them.
Invoked in City of Heroes: Scirocco is described as "the sort of person who called himself a freedom fighter instead of a terrorist".
UX in the first arc of Super Robot Wars UX becomes this, combined with "Hero with Bad Publicity", despite them being the heroes. It doesn't help that some of the villains in the governments are ready to sell Earth to the invaders.
In BrinkLa Résistance are fighting against the Founders who they think are hoarding resources and not doing enough for the people. Their enemies, Security, are just regular police trying to keep the peace who see Resistance as troublemakers. It's not helped by a lot of Unreliable Narrator.
The White Fang organization of RWBY. Some, such as Blake, see them as merely fighting for Faunas equality, while others, like Weiss, have felt the effects of their more dangerous actions and see them as terrorists and even genocidal.
Red vs. Blue has this in season 12, with the civil war between the Rebels and the Federal Army.
FUG from Tower of God, a fanatical religious crime syndicate hell-bent on killing Zahard and abolishing his ruling system. They go about it in such murderous ways that many in the Tower fear them, even though they do have a point somewhere: the current system is unfair and harmful to many. Even main characters 25th Baam and Ja Wangnan as well as Reasonable Authority Figure Lero-Ro see that.
In Sluggy Freelance, in the story "That Which Redeems", demonsinvade an alternative dimension populated by ridiculously Perfect Pacifist People. Torg and a handful of others try to form a resistance movement. Since the demons move from conquest of arms to more subtle tactics and propaganda (while still tormenting and killing the humans because, well, they're demons), and because the locals are willing to accept anything no matter how ridiculous if it seems to reduce the appearance of conflict, and they abhor the least bit of violence as much as the worst of it, the resistance is labeled in the media as "a bunch of pro-violence bozos working against the demonic visions of peace."
Quantum Vibe has the Space Pirate Jesus Hernandez raids Mercorp ships to fund a revolution on Io, and holds trials for the crews and passengers, with "penalties" that include airlocking or cutting off tongues.
It is not explored in great detail, but this trope is definitely in play with Iraqi terrorist/freedom fighter Oran in Broken Saints. He has been raised to believe that rebellion against the Western invaders is his duty, although he frequently has periods of doubt, where his devout religiosity makes him question his violent methods. Because of this self-doubt, the plot kind of leaves him alone about the matter after a couple of chapters, and treats him like a traditional Anti-Hero. It is also worth noting that we never hear specifics of what horrible things Oran may or may not have done in "service to his country".
In the Global Guardians PBEM Universe, the terrorist organization known as "Prime 8" is an army of gorillas, chimpanzees, and orangutans who all have a need to serious punish the humans. They are lead by a band of eight simian supervillains who a lot of the talking ape population consider heroes and freedom fighters, not criminals.
The Harry Potter ARG 'Magic is Might' has this set up, with the Order of the Phoenix being labeled 'The Rebellion' by the Voldemort-controlled Ministry of Magic.
The Equalists in the Sequel Series, The Legend of Korra. They see themselves as fighting back against benders who have been oppressing them, but they undercut their own moral authority by indiscriminately bombing Republic City and by targeting, of all groups, the last four airbenders (three of whom are children).
Bullock: You gave away state secrets to a terrorist!? Stan:(sheepishly) Freedom fighter?
In Challenge Of The Go Bots, when Fi-Tor is captured by the heroes, he appears rather noble, and clearly believes in his own side's cause. When he tries to destroy the transport ship carrying him away for interrogation, which would kill both him and the crew manning it, the heroes call him a maniac. He responds, "You mean 'patriot!'"
In the Season 2 Mandalore-trilogy of Star Wars: The Clone Wars the Separatists and the Death Watch are explicitly counting on this trope: Death Watch commits terrorist bombings on the planet, to make it appear that the Mandalorian goverment can't handle the situation on it's own, so the Republic would send clone troops to keep peace. This however would turn the terrorists into heroes in the eyes of the public, destabilizing the pacifist goverment, and resulting in the rebirth of the Mandalorian warrior culture.
Later in Season 5, this trope is Obi-Wan's main reason to object against Anakin's plan to train a group of rebels on Onderon.
A more popular portrayal of the Transformers lately is with Cybertron as a stagnant, caste based society. The Decepticons are to some extent fighting for freedom and a new, fair order. Unfortunately thanks to Megatron, it all got out of hand with many joining simply for the pleasure of opportunities for sadism and destruction.