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Merging the Branches

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A specific form of Cutting Off the Branches where events from several story branches or endings are declared Canon by a later installment, even though it is impossible for all these events to occur in the same playthrough of the previous game.
Overlaps with Third-Option Adaptation (which is about Taking a Third Option when adapting interactive works to non-interactive media). See also Broad Strokes.
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A Little Lily Princess inverts this due to adapting a novel into a medium with Story Branching and making some events lifted directly from the source material exclusive to some routes:
One of the most obvious ways by which this happens is that Sara remains friends with both Ermengarde and Lottie after her Riches to Rags in the novel, but Sara can maintain her friendship with only one of them in Act 2 of the game.
The food hamper party whose interruption is the cause of the Darkest Hour in the novel is here exclusive to Ermengarde's route and doesn't include Lottie. Ermengarde and Lottie are equally regular visitors of the attic in their respective routes. Ermengarde's route is also the only one in which Melchisedec plays enough of a role to be named, while the only Act 1 scene that mentions the existence of the rats, which also has Sara consider making friends with one, is exclusive to Becky's route. Becky's route mentions Melchisedec's family exactly once in Act 2.
Ermengarde's route is the one with the second act that is the most similar to the novel equivalent of Act 2, but Becky's is the closest in terms of actual ending.
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Star Ocean: The Second Story:
Numerous party members were mutually exclusive. You couldn't recruit Opera if you recruited Ashton (which also excluded you from recruiting Ernest since Opera is required to recruit him), you couldn't recruit Bowman if you recruited Precis, and both Dias and Leon were exclusive to who you chose as the main protagonist; Dias if you chose Rena, and Leon if you chose Claude. However, the japan-only sequel for the Game Boy Color, Star Ocean Blue Sphere, completely ignores this, and all of the previous game's party members show up as though all of them were recruited. The instruction manual for the third game also explicitly states that the Ten Wise Men were defeated by twelve heroes.
Two of Claude and Rena's endings three endings are subjected to this. The Japan-only sequel canonizes the Equal Affection Ending, where Claude and Rena explore space together on behalf of the Federation. The fifth game canonizes the Rena's Affection Greater ending, where Rena moves to Earth with Claude and states they're expecting their first child soon, implicitly moving it to after the events of Blue Sphere; one of that game's party members, Emmerson T. Kenny, is very strongly implied to be Claude and Rena's direct descendent. The Claude's Affection Greater ending, where Claude moves to Expel with Rena, falls to Cutting Off the Branches.
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Street Fighter Alpha 3 not only assumes most if not all of the endings from the second game to be canon, but most of it's own as well. M. Bison/Vega had a really bad day. Same goes for Charlie/Nash, since it's his Alpha 2 ending (where he's betrayed and killed) that is used as the basis for his return in Street Fighter V.
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Deus Ex: Invisible War uses a combination of the three possible but mutually exclusive endings of the first game. JC Denton merged with Helios, but this caused global communication to suffer a breakdown and the world descend into a period of war and economic depression known as "the Collapse", the Illuminati then used the resulting chaos during this time to consolidate their power.
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Installments of the Dawn of War series set after Winter Assault imply that the latter's true ending contains elements of both Ork and Eldar campaigns (Taldeer survives the Orks, Chaos and Necrons on Lorn V but is taken out by the Blood Ravens on Kronus in Dark Crusade), while Crull is defeated and his skull taken by Gorgutz 'Ead'unter (the Chaos faction takes it back from him in Dark Crusade).
Although the Orks didn't win in Dark Crusade, some fans refer to him with the full list of titles he gives himself for beating the six other factions (that is, Gorgutz 'Ead'unter Daemonkilla Deffkilla Bloodspilla Gunsmasha Ragescreama Ghostkilla). Despite losing, Gorgutz does survive and he absolutely is the sort of person who would claim those titles anyway.
Fanon holds that Retribution's ending contains elements of some of the others, mostly because they aren't directly contradicted by each ending: The Space Marines win and Gabriel becomes the new Chapter Master, it is implied that Sergeant Avitus was the traitor in Chaos Rising while Sergeant Thaddeus and the Force Commander were sent on a penitence crusade for resorting to using tainted war gear while remaining loyal, everyone else including Honour Guard Captain Apollo Diomedes, Sergeant Tarkus, Sergeant Cyrus, Techmarine Martellus and Librarian Jonah Orion are still with the loyalist part of the Chapter (Jonah also survives the wounds he receives in the beginning of Retribution) , the Imperial Guard showed up to help the Space Marines, the Eldar get Taldeer's soulstone back and help the humans bring down Kyras, the Orks use the distraction make off with the Judgement of Carrion to replace their downed Krooza, and Eliphas killed a bunch of things and managed to become a Daemon Prince (or at least survive the game). The only one that doesn't get included is the Tyranids, probably because they would have eaten everything in the sector.
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Jim Sangster's Doctor Who Novelisations style adaptation of "Dimensions of Time" has the dimensional instability result in the Eastender who gets between the Rani and Liz Shaw constantly flickering between Big Ron and Mandy, reflecting that both versions were filmed, and which one was used (Mandy) was based on an audience vote.
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Kindergarten 2 takes place after the first game's Omega Ending. However, some parts of the first game's other routes are present in the sequel, such as Monty having been confined to a wheelchair by the Janitor.
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Fear & Hunger: Termina takes this approach to several of the endings of its predecessor — for instance, it's made apparent from the Skin Bibles and August's existence that Enki and Ragnvaldr survived to get their Endings S, Ending C is implied to have happened through Le'garde resurfacing as the Kaiser, and the acknowledgement of the God of Fear & Hunger confirms that Ending A happened too.
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Bloodstained: Curse of the Moon 2 starts either the Final Episode or Episode EX (depending on how you finished Episode 2 the first time) with Zangetsu's allies from Curse 1 appearing and treating him as a longtime friend, which implies that the "Nightmare's End" ending is canon, and yet Zangetsu is ALIVE and NOT trapped in the world of Azure Striker Gunvolt so it's clear that this trope is in play.
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Castlevania III: Dracula's Curse has three potential partners for Trevor Belmont (Grant, Sypha, and Alucard). You can only have one partner at a time, and it's impossible to meet both Sypha and Alucard on the same playthrough. Castlevania: Symphony of the Night establishes that canonically, all four of them fought Dracula together. The 2017 Netflix adaptation opted for Trevor to join up with Sypha and Alucard, while Grant got Adapted Out.
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Ace Combat:
In Ace Combat Zero: The Belkan War, Cipher fights five out of eleven elite Belkan (well, only most of them are Belkan) squadrons in any given playthrough, with three of them changing per playthrough depending on your Karma Meter (e.g. whether Cipher fights Rot, Grun or Indigo in his first flight over the Round Table). However, the in-game Assault Records and later lore implies that at the branching points, Cipher faced all three respective squadrons at the same time, meaning he almost single handedly wiped out nine elite squadrons, not even including Gelb and Espada, who appear regardless of Karma Meter status.
Ace Combat 5: The Unsung War has a minor example with its more basic story branching. There are two points in the game where your answer to an otherwise-unimportant question asked by one of your wingmen determines which mission you go on afterwards, and to unlock the ADF-01 FALKEN superfighter, you have to play through the game at least twice and go through both branches. It's indicated that every mission happened anyway, even if the Wardog squadron didn't undertake them - the first branch starts with Wardog either defending an airstrip or dealing with a chemical attack at a civilian city, with mention of another squadron passing by to deal with the issue Wardog can't, and Aces at War: A History indicates that all five of the hangars the player needs to destroy to unlock the aforementioned superfighter were destroyed and raided by Osean forces, with them getting the full plans for the plane and having a completed example flown in an airshow a year after the events of the game.
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In Persona 2, you could meet most of the main cast of the first game, who imply that both the main quest and the Snow Queen quest happened, and also that the protagonist was there for both. Since you can't do both plotlines on the same save file, this is rather strange, though dialogue at the end of the Snow Queen quest implies that the cast are going to go and do the main quest afterwards, which still raises a lot of questions, since St. Hermelin is missing for the entire main quest...
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Sonic Adventure 2: The Hero and Dark paths each end in a similar place, with Tails fighting Eggman for the real Chaos Emerald while Sonic battles Shadow over the fake one. The Hero and Dark endings each imply their protagonists won their duels, but both lead into the Last Story. Some subtle editing shows how both endings are true: in the Hero ending, Eggman is seen swiping the real Emerald behind Tails' back while they assume he's unconscious, so whether he wins or loses, he winds up with the final Emerald. The Dark ending doesn't show the aftermath of either battle, simply cutting to Eggman triumphantly inserting the final Emerald into the machine, and beginning an Evil Laugh while, behind his back, an error pops up on the control screen, indicating something has gone wrong with the Eclipse Cannon firing (implied to be Gerald Robotnik's booby trap activating and seizing control of the colony). So either ending can lead into the Last Story, which has all seven Emeralds plugged into the machine, but the Eclipse Cannon not firing for one reason or another.
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Divinity: Fallen Heroes is a follow-up to Divinity: Original Sin II and features all six of the Origin Characters and Malady alive, thus ignoring the fact that in OS2 any of the Origin characters you don't recruit will be killed.
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Warcraft: The series did this for everything up to Warcraft III: Reign of Chaos (in which the campaigns happen sequentially). The second game took the first's Orc campaign as canon but with several Human story missions as still having happened instead of their Orc variants. The second game was treated the same way but with the sides reversed by its expansion. The second game's expansion is later treated as two sides of the same story, with the canon result of the final battle combining the endings. 3's expansion also has sequential missions and sets up the stage for World of Warcraft.
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Dark Souls II and Dark Souls III are predicated on both endings to Dark Souls happening - whether the Chosen Undead Linked the Fire or not, eventually someone would, and eventually someone wouldn't and it would need to be reignited. The Dark Lord ending was just another part of an endless cycle, and by the time of III, the world is actually becoming worn out from going through the periods of light and dark so many times.
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In Resident Evil, Barry doesn't appear in Chris' story after the opening scene, and Rebecca doesn't appear in Jill's game at all. According to the sequels, they all made it out of the mansion.
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In Fire Emblem: Shadow Dragon, several characters were only recruitable in gaiden (sidequest) chapters that required several playable characters to die to access them. In New Mystery of the Emblem, however, all returning gaiden characters except Nagi (who requires specifically Tiki to be dead in order to access her) are treated as if they joined Marth's army despite the fact that every playable character from the previous game survived to see the sequel.
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 Fire Emblem: Shadow Dragon & the Blade of Light (Video Game)
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Played with in Silent Hill 2. The canonicity of Silent Hill 4: The Room is somewhat vague, but it does feature the father of 2's protagonist mentioning that he hadn't heard from his son since the latter (James Sunderland) visited the titular town. Whether his father is referencing the first or second time his son visited Silent Hill is not specified, but either way, all of part 2's endings can account for this, from James deciding to start over with Maria, to him committing suicide, to him remaining in the town to revive Mary through occult means, to him purging his inner demons and leaving behind his old life to become a father figure to Laura. None of these possibilities is canon (according to Word of God, this choice is solely up to the individual player and no "official" answer exists), and part 4's attempt to provide a resolution doesn't in any way preclude the player from reaching their own conclusion as to James' ultimate fate.
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In the update to Devil Survivor 2, Record Breaker, the Triangulum arc follows a merger of the Kingmaker and Triumphant Restorer endings of the original narrative. In the original game and in the Septentrione arc of Record Breaker, it was impossible to have every character remain alive in any route, since at least one will die canonically in each one. In the recap of the Septentrione arc at the beginning of the Triangulum arc, it's revealed that everyone lives due to the merged endings.
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Mortal Kombat 1: This is the game's big reveal. Whereas the player is led to believe only the Liu Kang ending from Mortal Kombat 11: Aftermath is canon, it turns out that the Shang Tsung ending was spun off into an alternate timeline and the newly empowered Titan Shang Tsung has orchestrated the events of the game to conquer the multiverse. This is because the final battle from Aftermath caused time to split off into more branching timelines, including the one where Liu Kang became Keeper of Time, and the one where Shang Tsung became Keeper of Time. Then Liu Kang summons other Keepers of Time that originated from 11's timeline, revealing that even the arcade endings from that game are canon as well.
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In Pokémon Gold and Silver, Red fights with the original 3 starters (Charizard, Venusaur, Blastoise) and Pikachu, a team that is only possible without trades if the canonical game is Yellow. However, Blue's lineup is his team from Red and Blue minus his starter. Other issues of exactly what Pokémon Red got during his journey are sidestepped by filling out the rest of his team with required encounters (one of the Snorlaxes blocking the way to Fuchsia City) or gifts (an Espeon evolved from an Eevee found at Celadon Mansion in the originals, a Lapras given by a worker at Silph Co. during Team Rocket's takeover in the remakes).
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Escape Velocity Override told its story "Rashomon"-Style according to Word of God. Officially all the endings happened.
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Drakengard 3 itself is an example of this. Supplementary materials reveal that the timeline that leads directly into Drakengard is a combination of endings A and B; Zero forms a pact with the flower to save Mikhail from poisoning as in Ending B, and then Zero kills One in a duel before being killed by a male clone of One as in Ending A.
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In Tales of Symphonia, the manga adaptation merges bits and pieces of the Kratos, Zelos and Colette endings and has each of them give Lloyd the special item that he receives only from their ending in the game:
In the Flanoir scene, Lloyd first talks to Colette. Colette leaves to go check in at the inn, then Kratos shows up to talk to Lloyd and play out his Flanoir scene.
Lloyd also talks to Zelos in this same night (Again, playing out his Flanoir scene from the game), but the conversation only appears in a bonus chapter.
When Zelos betrays the party at the Tower of Salvation, Lloyd and company have a short battle against him right then and there, much like in Kratos’s route. However, unlike in the game, he doesn’t die during this scene.
The night before the party enters Torent Forest to release Origin’s seal, Lloyd talks to Zelos. However, Zelos doesn’t offer to join Lloyd on his journey to collect the Exspheres, unlike in the game.
After Origin’s seal is released, Colette is the one that gets possessed by Mithos.
Both Kratos and Zelos join the group for the final showdown with Mithos, which isn’t possible in-game.
Unlike in the game, when Lloyd departs on his journey to collect all the Exspheres, he plans to go alone (Which isn’t possible in-game; he made plans to have his closest ally come along with him back during the Heimdall night. However, just before he leaves, Colette suddenly shows up at the last second, wanting him to take her along with him, cementing herself as the closest ally in this adaptation. This is also apparently the canonical ending according to the sequel. Overlaps a bit with Third-Option Adaptation in that another change, Yuan coming with them to the final battle, actually isn't possible in any of the endings.
The OVA adaptation also could be argued as such. It sticks to the Colette route for the Flanoir scene (The Heimdall night never appeared in this adaptation, nor did Mithos taking over Lloyd’s closest ally). However, at the very end, just before the two set out to collect the Exspheres, Zelos and Sheena both show up unexpectedly, wanting to join in.
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Two of Claude and Rena's endings three endings are subjected to this. The Japan-only sequel canonizes the Equal Affection Ending, where Claude and Rena explore space together on behalf of the Federation. The fifth game canonizes the Rena's Affection Greater ending, where Rena moves to Earth with Claude and states they're expecting their first child soon, implicitly moving it to after the events of Blue Sphere; one of that game's party members, Emmerson T. Kenny, is very strongly implied to be Claude and Rena's direct descendent. The Claude's Affection Greater ending, where Claude moves to Expel with Rena, falls to Cutting Off the Branches.
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Ace Combat 5: The Unsung War has a minor example with its more basic story branching. There are two points in the game where your answer to an otherwise-unimportant question asked by one of your wingmen determines which mission you go on afterwards, and to unlock the ADF-01 FALKEN superfighter, you have to play through the game at least twice and go through both branches. It's indicated that every mission happened anyway, even if the Wardog squadron didn't undertake them - the first branch starts with Wardog either defending an airstrip or dealing with a chemical attack at a civilian city, with mention of another squadron passing by to deal with the issue Wardog can't, and Aces at War: A History indicates that all five of the hangars the player needs to destroy to unlock the aforementioned superfighter were destroyed and raided by Osean forces, with them getting the full plans for the plane and having a completed example flown in an airshow a year after the events of the game.
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Melty Blood declares a combination of two endings (Ciel's and Kohaku's) plus events that never actually happened in any canon route.
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Persona:
In Persona 2, you could meet most of the main cast of the first game, who imply that both the main quest and the Snow Queen quest happened, and also that the protagonist was there for both. Since you can't do both plotlines on the same save file, this is rather strange, though dialogue at the end of the Snow Queen quest implies that the cast are going to go and do the main quest afterwards, which still raises a lot of questions, since St. Hermelin is missing for the entire main quest...
In the PSP Updated Re-release of Persona 3, players could choose between either Elizabeth or Theodore as the Velvet Room assistant, so their appearances are mutually exclusive. In Persona 4: Arena Ultimax, both Elizabeth and Theodore appear and have plot significance, and in Persona Q: Shadow of the Labyrinth, the two of them also appear, with the protagonist familiar with both of them, indicating that canonically both served as assistants (despite the fact that Theodore can only be selected as an attendant if one plays as the female protagonist exclusive to Portable).
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Fire Emblem: Thracia 776:
In Fire Emblem: Genealogy of the Holy War, Lachesis, like all other first-generation female characters that don't have a plot lover, has two children with whomever marries her. The midquel, Thracia 776, features both her children as playable characters, but heavily implies they have different fathers, something not possible within the game mechanics of Genealogy. Namely, Beowulf is canonically Diarmuid's father, and Finn is canonically Nanna's. Beowulf's lover conversation with Lachesis in Genealogy's Chapter 5 implies he leaves her so she can be with Finn, but gameplay-wise he'd still father both her children.
A case of this being averted in the finished product, but played straight in earlier development: Genealogy features "substitute" units, who only show up if a mother in the first generation died or got left unmarried, who replace the children of that mother are usually somewhat inferior to the characters they replace. In Thracia's story proper, the game seems to run with the idea that the substitutes don't exist; at the very least, the kids belonging to Erinys, Lachesis, Sylvia, and Brigid all appear or get referenced at some point, and none of the substitutes appear. However, there are several portraits, Dummied Out in the final product, that unmistakeably belong to several substitute characters—specifically, Asaello and Daisy (replace Brigid's son Febail and her daughter Patty), Femina (replaces Erinys's daughter Fee), and Jeanne (replaces Lachesis's daughter Nanna). This suggests that at some point, the intention was to have the substitutes exist in the same timeline as the other units.
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In The Elder Scrolls series: Daggerfall has seven mutually exclusive endings. However, later works starting with Morrowind, reveal that all of the endings, even one that was cut from the final version of the game, happened. This is explained In-Universe as a Cosmic Retcon/Time Crash known as the "Warp in the West". However, none occurred to the same extent they would have individually. For example, instead of one political power dominating the region, the dozens of city states merged into four with all still under the banner of the Empire. Mannimarco successfully ascended to godhood, but in a rather minor station,note Some texts even claim that he was later restored to mortality while also leaving a "mortal" version behind who leads the cult that worships the god version. Numidium doesn't go on a Tamriel-destroying rampage, but is rendered forever non-functional through unexplained meansnote although it may have something to do with that the one ending to not have any indications it didn't happen in its entirety — the Underking finally dying permanently — also leads to the Numidium being rendered non-functional (the Underking needed the Numidium's power-source to die). Nobody in the region actually has any idea how any of this happened; they all woke up one morning in the new status quo with no memory of the previous two days. The Warp itself happened due to the Numidium being a Mechanical Abomination built by the disappeared Dwemer to act as a refutation of the Gods, including the God of Time; just being active royally messes up the very idea of time in the area.
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In Fire Emblem: Genealogy of the Holy War, Lachesis, like all other first-generation female characters that don't have a plot lover, has two children with whomever marries her. The midquel, Thracia 776, features both her children as playable characters, but heavily implies they have different fathers, something not possible within the game mechanics of Genealogy. Namely, Beowulf is canonically Diarmuid's father, and Finn is canonically Nanna's. Beowulf's lover conversation with Lachesis in Genealogy's Chapter 5 implies he leaves her so she can be with Finn, but gameplay-wise he'd still father both her children.
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Mega Man X4 plays X and Zero's stories separately, and they don't interact with one another at any point except in X's ending animated cutscene. Either way, the player has to defeat both Colonel and General, the Repliforce leaders. Mega Man X5 confirms through the intro and dialogue from Spiral Pegasus (one of the eight Maverick Bosses) that canonically Zero was the one who fought and killed Colonel and thus in turn had to fight and kill Iris, while it's hinted that X fought General.
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In Ace Combat Zero: The Belkan War, Cipher fights five out of eleven elite Belkan (well, only most of them are Belkan) squadrons in any given playthrough, with three of them changing per playthrough depending on your Karma Meter (e.g. whether Cipher fights Rot, Grun or Indigo in his first flight over the Round Table). However, the in-game Assault Records and later lore implies that at the branching points, Cipher faced all three respective squadrons at the same time, meaning he almost single handedly wiped out nine elite squadrons, not even including Gelb and Espada, who appear regardless of Karma Meter status.
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Its prequel, Deus Ex: Human Revolution, inverts the trope by having all of the possible endings plausibly lead to the events of the first game: telling the truth about the conspiracy leads to augments getting banned (explaining why they're everywhere in DXHR but rare in DX1), lying on Taggart's behalf leads to a major reform of the United Nations (which could lead to DX1's UNATCO), lying on Sarif's behalf removes regulations on augs which scares the Illuminati into finding stronger means to control the populace (which leads to the creation of the Gray Death virus), and the fourth option kills everyone in the building (which would explain why nobody exclusive to DXHR appears in DX1). Its sequel, Deus Ex: Mankind Divided, subverts this by following as though none of them happened.
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The Legend of Zelda: Majora's Mask somehow manages to do this to itself. Completing every sidequest in the span of a single three-day cycle is impossible due to two major quests being mutually-exclusive, and would be prohibitively difficult even if it could be done, so once you'd gotten the reward for a given sidequest, there wasn't much incentive to repeat it on subsequent cycles. The game's ending implies that every sidequest you ever completed in the game was ultimately merged into the final timeline where Skull Kid and Majora's Mask were defeated.
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Drakengard turned out to be a case of this. Initially, there were five endings in the original game. Ending A, the one where they stop the Big Bad and set everything back to normal, was the only one that could reasonably lead to Drakengard 2 (since all the others featured The End of the World as We Know It and/or the protagonist disappearing into a portal), but Ending E, the one where the protagonist and his dragon follow an Eldritch Abomination through the aforementioned portal into 2003 Tokyo, defeat it there, then get unceremoniously shot down by a Japanese fighter plane, is revealed to be the ending that leads to NieR. Background material released around the same time as Drakengard 3, however, reveals that the timeline of Drakengard is pretty similar to our own, just with a calamity called the "Great Apocalypse" happening around A.D. 856; after the time of the second game, around A.D. 1117, the Drakengard world starts going back down a path similar to the real world's again, with only minor changes such as "Black Friday" being "Black Thursday" instead. Up until 2003, when the sky opens up over Tokyo, spitting out a giant grotesque creature and a smaller red dragon intent on killing it...
Drakengard 3 itself is an example of this. Supplementary materials reveal that the timeline that leads directly into Drakengard is a combination of endings A and B; Zero forms a pact with the flower to save Mikhail from poisoning as in Ending B, and then Zero kills One in a duel before being killed by a male clone of One as in Ending A.
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Deus Ex:
Deus Ex: Invisible War uses a combination of the three possible but mutually exclusive endings of the first game. JC Denton merged with Helios, but this caused global communication to suffer a breakdown and the world descend into a period of war and economic depression known as "the Collapse", the Illuminati then used the resulting chaos during this time to consolidate their power.
Its prequel, Deus Ex: Human Revolution, inverts the trope by having all of the possible endings plausibly lead to the events of the first game: telling the truth about the conspiracy leads to augments getting banned (explaining why they're everywhere in DXHR but rare in DX1), lying on Taggart's behalf leads to a major reform of the United Nations (which could lead to DX1's UNATCO), lying on Sarif's behalf removes regulations on augs which scares the Illuminati into finding stronger means to control the populace (which leads to the creation of the Gray Death virus), and the fourth option kills everyone in the building (which would explain why nobody exclusive to DXHR appears in DX1). Its sequel, Deus Ex: Mankind Divided, subverts this by following as though none of them happened.
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Repeatedly used in the Diablo series: in the single-player, you must choose which character to complete the game with, but the respective next installment declares that all playable characters participated in the previous one's plot. This is possibly justified in that the Co-Op Multiplayer with all available classes represented is viewed as canon, even for offline play.
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Command & Conquer: Red Alert 3: The Allied campaign was the canon ending, but in the expansion Commander's Challenge, Moskvin has a minor Freak Out on facing the Shogun Executioner (which only appears in the Rising Sun campaign).
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In Ultima IV: Quest of the Avatar, you have eight possible party members but you can never recruit the one of the same class as yourself. Nevertheless, all eight are regarded the Companions of the Avatar in later installments.
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Tsukihime:
Melty Blood declares a combination of two endings (Ciel's and Kohaku's) plus events that never actually happened in any canon route.
Tsukihime's other sequel, Kagetsu Tohya, justifies all the routes being canon at once by having the story take place in a dream, where real-world logic is of course out to lunch. Those parts of it that take place outside the dream seem to suggest either Ciel's or Arcueid's ending, however. It also includes a number of side stories that explicitly take place in some of the other endings.
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Every ending of every game in the Henry Stickmin Series is canon. This includes Infiltrating the Airship and Fleeing the Complex, which have very drastically different endings depending on the choices done during those games.note Completing the Mission is entirely dependent on the endings obtained in both Infiltrating the Airship and Fleeing the Complex. According to Word of God, if one ending were declared the "true ending" then it would undercut the series' Choose Your Own Adventure roots.
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Star Wars Legends reference books establish that the Exile, the Player Character of Knights of the Old Republic II: The Sith Lords, is female but also had the Handmaiden on her team, which in-game is only possible for a male Exile. Had the game not been Christmas Rushed, recruiting Handmaiden would have depended on the player character's alignment rather than gender, much like with Mira (light siders) and Hanharr (dark siders), and with Visas Marr (who normally joins regardless of alignment or gender) being the dark side alternative; presumably, this would mean the Disciple, who is the alternative to Handmaiden for female characters in the released game, would have also joined regardless of gender or alignment.
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In the Last Story mode of Shadow the Hedgehog the plot appears to consider a number of events canon, such as the President being evacuated to the GUN Fortress, Eggman claiming Shadow to be an Android, and the majority of the cast traveling to the Black Comet. These are all plot points that cannot happen in a single playthrough of regular Story Mode's branching paths, implying that regular story mode is always just "what if" scenarios that merely represent Shadow's real journey, regardless of your chosen path. Nevertheless, the Word of God claims that the "True Hero" path is canon. Make of that what you will.
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Fate/hollow ataraxia, the direct sequel to Fate/stay night, has a bizarre conglomeration of events from mutually contradictory routes making up its backstory. This is actually a plot point though, and part of the story's progression is figuring out just what the hell is going on. Turns out it's a merged timeline that came about due to a mishap involving Rin's attempt to recreate the Jeweled Sword of Zelretch, which is capable of accessing alternate timelines.
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