In RealTimeStrategy games, the various factions are usually unified, monolithic entities. But fighting the same enemies in battle after battle gets boring. So the developers will often contrive some reason for fighting against your own side in single-player scenarios. Usually this involves betrayal on one or both sides.

Also, the campaign mode in an RTS game often serves as an introduction to the multiplayer game. So the game is obligated to not only force you to play each side, but also to contrive reasons to encounter each possible matchup. Which includes fighting your own side.

A storyline-motivated form of the MirrorMatch. Compare EnemyExchangeProgram and EnemyCivilWar.
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!!Examples:
* In ''{{Achron}}'' the remnants of the human fleet find themselves fighting against a section of the military that seems to have its own objectives. In the Grekim campaign one of their leaders decides he would be best to lead their race, and hunts down the others. The Vecgir end up fighting against their own when they face a group of runaways that went and joined the Grekim.
* In ''VideoGame/{{Warcraft}}'' and ''VideoGame/{{Warcraft}} II'', several Alliance vs. Alliance missions were centered around traitors who for some reason decided that siding with the evil Orcs was in their best interest. The Orc vs. Orc missions involved a power struggle between two major Orc leaders, Gul'dan and Doomhammer. Then, Beyond the Dark Portal came along, and everything got complicated.
** ''VideoGame/{{Warcraft}} III'' had a fair bit of this as well:
*** The end of the Orc campaign involved squaring off against a camp of corrupted Orcs. Though the enemy orcs were much stronger counterparts of your own, they still matched up well enough.
*** ''The Frozen Throne'', the expansion pack for ''Warcraft III'', had a three way war between the Forsaken (Undead) VS. Scourge (Undead) VS. Dread Lord Rebels (Undead) missions, and a couple Blood Elf vs. Alliance missions, the Blood Elves being a [[CosmeticallyDifferentSides visually different but statistically identical splinter faction of the Alliance forces.]]
** The entire [[WorldOfWarcraft Mists of Pandaria]] expansion his been building up to this situation for the Horde. It eventually comes down to Vol'jin and the other leaders of the Horde against Garrosh and his Kor'kron. [[spoiler: Even after Vol'jin is named the new Warchief it appears that this situation could potentially pop up again. Speaking to Sylvanas following the raid shows she has no intention of listening to a troll and has every intention to see what she can get away with. Lor'themar also expresses concern regarding Sylvanas.]]
* ''StarCraft'' had this, sometimes extensively, in all the campaigns, though especially the Terrans. In the first campaign the player was a rebel leader against the Confederacy, in the ''Brood War'' expansion's campaign the player was a UED commander coming to bring the Koprulu sector colonies [[TheWarOfEarthlyAggression under earth's control]], while in ''VideoGame/StarcraftII'' you play as the leader of the rebellion against the Terran Dominion established with the help of the first game's player. The Zerg on the other hand have one mission in their first campaign where a slain cerebrate's brood has gone feral and must be destroyed, and in the expansion the Overmind is dead and the remaining cerebrates are fighting with Kerrigan for control of the remaining swarms. In the case of the Protoss Tassadar and his forces were declared heretics for associating with the Dark Templar, though they end up saving what's left of their entire species after the Zerg invade their homeworld.
* The ''VideoGame/CommandAndConquer'' games have this as well.
** Tiberium Dawn had an inversion in the Nod campaign where you had to take out a GDI base with stolen GDI equipment because a traitorous commander sent your normal forces halfway across the world.
** The Nod campaign of Tiberian Sun starts off as a civil war between various factions of the group. Later there's a subversion where you hijack GDI equipment to fight the Forgotten (who are using Nod equipment).
** The Soviet campaigns in Red Alert 2 and 3 necessitates the elimination of another Soviet general whom the Soviet leader has declared [[YouHaveOutlivedYourUsefulness inconvenient to keep around.]] Of course it's only a matter of time before they try to do the same to you.
** And in Red Alert 3, when playing as the Allies [[spoiler:you have to attack an Allied base under the command of the Japanese android US president]].
*** Red Alert 3: [[ExpansionPack Uprising]] has former Crown Prince of Japan Tatsu, now cooperating with the victorious Allies, going against the Japanese generals. [[spoiler:And once you've got rid of the rogue Japanese generals, he then goes and betrays you and uses all the stuff stolen from those generals to attack you!]]
** In ''CommandAndConquerGenerals'', the only faction that ever outright fights their own side in the ''main'' campaign is the GLA. Technically, you DO do this, but it's {{handwaved}}: Rogue Chinese General, GLA using captured USA Equipment from an abandoned base, et cetera. Given that they're a massing of factions rather than an army of a particular country, this makes sense. The "Generals Campaign", however, pits a general of your choosing against each of the other available generals in sequence, including the ones that share your nationality. With there being 6-7 AI generals to choose from (In a non-modded version of the game, the Infantry and Demolition general levels are DummiedOut), in a campaign where 6 are randomly chosen to fight you, it is guaranteed that you will go up against someone who shares your nationality.
** In VideoGame/CommandAndConquer 3, Nod missions at Sarajevo and Ayers Rock involve the player [[MagnificentBastard Kane]]-loyalist Nod army facing off against rogue Nod soldiers.
*** Also done well in the Kane's Wrath expansion, the first Act involves vanilla Nod forces fighting against the Black Hand, a subfaction.
** Command and Conquer 4 has you fighting your own faction no matter what side you choose. On top of that, the GDI campaign doesn't have you fighting renegade GDI soldiers, you ARE the renegade GDI soldiers.
* The ''TabletopGame/{{Warhammer}}'' World is so discordant that it actually makes sense for almost anyone to be fighting themselves.
** The same for the ''TabletopGame/{{Warhammer 40000}}'' Galaxy.
*** They've now released an ''expansion'' for Warhammer in White Dwarf focusing on civil war, [[TheDevTeamThinksOfEverything detailing rules for all the possible reasons a faction would have for fighting themselves.]]
*** One White Dwarf magazine article featured a battle which the writers wanted to be the biggest battle possible. Unfortunately, the two biggest armies the writers had lying around were Space Marines and Imperial Guard, who are nominally on the same side. They came up with the explanation that an extraordinarily powerful psychic had arisen on an Imperial planet, who could mind control the entire planet, including its Imperial Guard contingent. The Space Marines were sent in to put him down.
*** The troops of the Ecclesiarchy also seldom need a reason more specific than "might be corrupted by Chaos" to battle allied Forces. The White Dwarf Scenario mission for the Grey Knights "Wipe out the Infestation" states that a Catachan expedition force might have been exposed to Chaotic influence... and so the Grey Knights have to deal with it appropriately.
*** Also the Blood God Khorne is known for enjoying bloodshed regardless of whose blood is shed. Followers of Khorne rarely disappoint their Master in this, whether they slay their enemies or be slain themselves.
*** In the fantasy setting, Witch Hunters are feared by friend and foe alike for their "burn first, ask questions later" attitude.
* Speaking of which ''DawnOfWar'' ''Dark Crusade'' features two scenarios with either the Imperial Guard fighting the Blood Ravens or the Blood Ravens fighting the Imperial Guard because each has their orders concerning Kronus and neither will give ground even to their own Imperial allies.
** And of course it happens again in ''Soulstorm'' this time between the Imperial Guard, the Blood Ravens, and the Sisters of Battle.
** The first case also has an interesting example of RewardedAsATraitorDeserves. When assaulting the Imperial Guard's home province as the Blood Ravens, one of the optional objectives is to kill an officer in charge of a certain regiment. The regiment will immediately switch to your side and fight against their former comrades. However, the after-battle text will indicate that those guardsmen whom you killed were buried with full honors for doing their duty, while the traitors were all executed.
* Happens a few times in ''VideoGame/SupremeCommander'', either due to corruption by Seraphim artifacts or internal politics. The expansion pack goes a step further, by having the Aeon Illuminati split completely into those who join up with the Seraphim, and those who join with the UEF and the Cybran Nation to try and save humanity.
** Notably, it isn't until the very last mission of the expansion pack that a UEF-UEF battle takes place, though during any mission, you have the option of capturing enemy units (or better still, factories), and gaining access to that tech tree. One entertaining example is capturing a Seraphim factory in the fourth mission of the expansion and building Ahwassa experimental bombers.
** And with proper preparations (a few Salvations, Experimentals or an ACU with a nuclear tactical missile launcher) the UEF-UEF battle will be one of the shortest in recorded history.
* WorldInConflict has Soviet special units take over an US base and use an absurd number of captured US vehicles in an attempt to attack New York. However, there is no chance of fighting your own faction in multiplayer.
* ''RiseOfLegends'' inverts this: most missions have you fighting an enemy using the same units as you are, or dark glass versions in the Alin campaign. Only a few missions have inter-factional warfare, and all but two amount to skirmishes.
* The ''VideoGame/AgeOfEmpires'' series has some of this, most memorably in the Montezuma campaign of ''Conquerors''. In the second scenario, after you defeat the Tlaxcala, your allies declare war on you.
** Barbarossa's campaign in ''VideoGame/AgeOfEmpiresII: Age of Kings''. The second mission involved attacking Poland without a Town Hall. True to history, you end up betrayed by Henry the Lion ''twice'' and end up having to deal with him in addition to existing obligations.
** It's actually very common in ''Age of Empires'' and its sequel, often when your civilization is fighting a rival state of the same civilization (e.g. Athens vs. Sparta, France vs. Burgundy).
** The first Salah ad-Din scenario has the Egyptians start off as your friend, then declare war on you, then become your friend again when you convince them you ''really are'' only going through Cairo to go kick some Crusader asses.
* ''VideoGame/AgeOfMythology'''s campaigns is a series of this. The reason for this is that the only consistent units that you control are a band of heroes who are traveling the ancient world in order to [[spoiler:stop the BigBad from unleashing [[SealedEvilInACan Kronus]]]], and that you raise armies from the people of where you happen to be. The villains do this as well, meaning that most battles involve the same units-the only difference being the gods worshiped by either side.
** The expansion starts of fairly normal, but then turns into this again when it turns you've been fighting for the wrong side.
** Of course, the main game has a dream sequence where you join the legions of Hades to fight the "Evil Empire", that being [[spoiler: Arkantos's lovely seaside kingdom of ATLANTIS!!!, packed to the gills with Olympian heroes.]]
* In the StarWars RTS Force Commander you're arrested, and you have to walk up to storm troopers who are more loyal to you than to the Empire in order to escape (it's the only level in the game in which there is a unit on the map to represent you). After that, you completely switch sides.
* Completely averted in ''CompanyOfHeroes'', where even in multiplayer you can never fight your own faction. This holds true in the expansion pack ''Opposing Fronts'' which added two new factions that still cannot fight a civil war. In fact, in ''Opposing Fronts'' multiplayer, the Americans and British factions must always fight on the same side, as must the two German factions (Wehrmacht and Panzer Lehr).
* Quite interestingly played with in ''StarWarsBattlefront II'', in which one mission of the 501st's campaign involving playing as Imperial Stormtroopers fighting an army of old Republic Clonetroopers on Kamino
* In ''Earth 2150'', playing as the Lunar Corporation (who were allied with the UCS) had one mission where you were both on the same map fighting the enemy together when a virus corrupted the UCS programming, turning ''every UCS unit on the map against you.''
* In ''VideoGame/ActOfWar: Direct Action'', the last two missions have you going up against Consortium troops exclusively using US Army equipment and uniforms. It's used more often in the ExpansionPack, ''High Treason'', with the final mission even featuring Consortium troops using Task Force Talon equipment for the first time.
* ''VideoGame/{{Homeworld}}: Cataclysm'' has an enemy whose main weapon is an infection beam that can instantly convert your units and send them back against you.
* ''RepublicTheRevolution'' features this as a late-game mission arc - a trusted ally leaves with half your agents, and you have to erode their support to recruit them back.
* ''VideoGame/HeroesOfMightAndMagic IV'' took this to really extreme levels when ''all six'' campaigns of the original game had the main enemy of the same faction as the player. Not so much in the expansions, though.
** ''ClashOfHeroes'' does the same thing, but in this case it's justified--the demon plan is to create a civil war, and they're not the one's behind the idea in the first place. There's also the bounties, who are all criminals.
* The first faction you need to destroy in BrutalLegend is an EvilCounterpart army of human slaves who refused to defect from [[BigBad Doviculus]]' rule, led by [[TheQuisling General Lionwhyte]].
* SwordOfTheStars doesn't have a campaign, but the very detailed fluff makes a point of explaining how the otherwise-unified races might have multiple factions in play:
** Far-flung human colonies attempt to declare independence, and refuse to take central command's "no" for an answer.
** The Tarka's complex hierarchical society is highly prone to political warfare under normal circumstances, this can easily boil over into military conflict.
** A [[BeePeople Hiver]] "princess" may get too big for her boots and attempt to wrest power from the existing Queen.
** Two Liir factions can start a conflict if each considers the other Suul'ka (roughly, "soulless")
** Zuul are by nature territorial and aggressive, infighting of various magnitudes is common.
** Morrigi can end up at each other's throats if two sufficiently powerful trade cartels end up vying for trade routes.
** In the second game the six races have more or less formed unified factions, but it's still possible in game for planets or even entire provinces to rebel.
* ''[[Videogame/BattleZone1998 BattleZone II]]'' has you destroy a [[DefectorFromDecadence splinter faction]] of the International Space Defense Force who wants peace, [[MyCountryRightOrWrong should you stay loyal]] to [[GeneralRipper General Braddock]]. If you join the Scions, you will fight a renegade commander who does not share [[BigGood Padisha Burns]]' vision for the future.
* Three of the episodes so far in ''VideoGame/MarchOfWar'' focus on civil wars fought between the various factions: Exalted Inferno, Tropical Thunder and African Sunrise.
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