The Reapers in the Mass Effect series incorporate a galactic-scale Batman Gambit into their life-cycle. They leave highly advanced technology around the galaxy as well as the Citadel, the largest, most advanced space station in existence to ensure that races develop along technological and cultural paths they desire. especially with regards to the Citadel, which invariably becomes the cultural center of any empire Then, possessing the technology to counter what they left behind, they quickly eliminate all life in the galaxy and melt down several million members of any species they find to make more Reapers. One could say that the Reapers are the living embodiment of the Batman Gambit. It's telling that all of their major defeats come about because somebody didn't follow the script.
In between Mass Effect 2 and Mass Effect 3, the Illusive Man pulls off numerous Batman Gambits to either cripple or wipe out anyone who can stand against him, including The Shadow Broker, with the original killed and Liara's network being greatly harmed and Aria T'Loak. This is to allow him to focus all his energy on his primary Batman Gambit: to take control of the Reapers ensuring human dominance. The first goes off magnificently. The second fails because, as magnificent as his mind was, it was still a human mind going against Eldritch Abominations that have been doing this for billions of years. He ends up indoctrinated and becoming their Unwitting Pawn.
Anders's plan at the end of Dragon Age II is basically to provoke the Templars into discrediting themselves by blowing up the Chantry, after which Meredith orders the entire Circle of Magi executed for a crime they didn't commit. Anders makes no effort to defend himself and will even let Hawke kill him, but Meredith loses any interest in him once she has an "excuse" to wipe out the Circle. She'll even let him fight with the Templars if Hawke's maxed out his Rivalry. When word of this spreads beyond Kirkwall, it prompts a full-scale Civil War.
Isaac pulls this on both Hector and Trevor in Castlevania: Curse of Darkness. He lures Hector (to whom he serves as a worthy opponent) along with the promise of eventually facing him in battle, and at the same time draws Trevor's attention. When he slips into the Infinite Corridor, Trevor is forced to let Hector into it... which leads to Hector accidentally breaking the seal on Dracula's Castle, Isaac's goal the entire time.
Of course, ultimately, we learn who the real wirepuller is. It's Dracula, of course; he'd be playing Gambit Roulette if he didn't already have his hooks deep into Hector and Isaac's psyches and thus a much greater chance of success than the average Yagami. The entire game is triggered by Dracula's effort to resurrect himself, to wit — raise the castle with Isaac's yanking of Hector and Trevor, have Isaac stab that damn Belmont, then possess Hector when Hector finally gets sick of this nonsense and kills Isaac, thus sealing the curse. Alas, he wasn't counting on Julia being the only one in the game with a clue.
Also, in Castlevania: Lament of Innocence, Mathias Cronqvist used Leon Belmont to kill Walter Bernhard to absorb his soul. At the end, Mathias slaps you in the face with the knowledge that he will become Dracula, Lord of the Vampires... The entire plot was designed so that he could become Dracula.
The entirety of Castlevania: Lords of Shadow 2 is one massive one run by Alucard and Dracula. Satan and Zobek were too afraid to come out while Dracula was in the fullness of his power. So Alucard nearly kills Dracula, both fully aware that the centuries spent recovering his powers would fragment Dracula's mind, concealing the gambit from his enemies, and allowing Zobek to believe he could dupe Dracula into killing Satan and/or vice versa, allowing Zobek to clean up the survivor, when in actuality, leaving both Satan and Zobek vulnerable to Alucard and Dracula working together.
In the Thief II fan mission "All Torc" and its sequel "Stones and Glass Houses", the Keepers use a Batman Gambit to ensure that repercussions from one of Garrett's thefts in Thief: The Dark Project are resolved.
In Overlord I, the game turns out to be a Batman Gambit designed to allow the previous Overlord to easily return to his place in case he was "defeated", by taking over the body of the Wizard who helped slay him, manipulating one of the heroes who defeated him into becoming his temporary successor, and corrupting the other heroes so the new Overlord would be forced to eliminate them.
Metal Gear Solid features a hastily improvised Gambit (developed by the bad guys' resident psychic, sensibly enough) which revolves around a single-use keycard which will toggle a nuclear weapon from "active" to "inactive" or vice-versa. The bad guys seem to accept that facing off against the hero is a suicidal masquerade to set up deathbed conversions and make the plan convincing.
All of the events within the PlayStation 2Shinobi turn out to be one big Batman Gambit orchestrated by the Final Boss Hiruko: He manipulated Hotsuma into defeating Yatsurao so that the villain could absorb the countless number of souls that were subsequently released from the fallen giant. And he intended from the very beginning for Hotsuma to gather all of the souls of each foe he had sent to take him out, at which point he'd defeat Hotsuma and take all those souls for himself.
In Dot Hack GU In what is possibly the longest to ever occur in gaming, Ovan uses a Batman Gambit that spans three games in order to make Haseo become strong enough to destroy him.
If you count the anime — .hack//ROOTS — then it takes even longer. And Ovan has to step in at one point to make corrections to Haseo's development.
In Shin Megami Tensei III: Nocturne, the Labyrinth of Amala subquest has you tasked with defeating the ten Fiends and returning the Candelabrum they had stolen to Amala. If you complete the Labyrinth of Amala (it is optional) then the whole thing is revealed to be a Batman Gambit orchestrated by none other than Lucifer himself. The Fiends had never stolen the candelabrum; the entire thing was set up as a training exercise to create a new demon that would be strong enough to lead the armies of Deep Amala in an war against God Himself, as well as a test to see if you had the fortitude to fully embrace your demonic side and become Deep Amala's champion.
From another Shin Megami Tensei game Persona 4 (which is about a murder mystery). Prodigy Detective Naoto Shirogane devises a plan to confirm his or rather her suspicions that the police caught a copycat killer, not the real killer. She sets herself up as bait for the kidnapper, confident that the Investigation Team will rescue her. Kanji lets Naoto have it for coming up with such a dangerous plan, while Yukiko (the first to figure out Naoto's plan), points out that if not for that, they likely wouldn't have realized that the culprit is still at large.
The entirety of Assassin's Creed is actually two giant Batman Gambits. The first, planned by The Dragon, Robert de Sable, involves using the Assassins' killing of his lieutenants, all of whom are important members of Saladin and Richard the Lionheart's respective support networks, to unite the Saracen and Crusader armies to crush the Assassins. The second is planned out by Al-Mualim, who plans to have Altair kill all of the Templars who knew about the Piece of Eden, because he himself is a Templar plotting to take over the Holy Land for himself.
And all that was planned by Abstergo to have Desmond reveal the locations of the Pieces of Eden. By then the entire plot becomes one huge Mind Screw: Abstergo are the Knights Templar who secretly are behind every technological innovation EVER, the Assassins still exist and try to stop them, Lucy might or might not be one of them (it turns out she used to be an Assassin before becoming a Templar mole), and then there's the scribbling on the wall...
Assassin's Creed Black Flag takes it to another level entirely. Past and present incarnations of Roberts are manipulating Templars and Assassins on behalf of a third group, whose purpose is to get the present-day protagonist in a position where their body can be taken over by Juno. It only fails because Juno isn't quite powerful enough yet to do it.
In Pokémon Black 2 and White 2, at least part of Ghestis' plan is a Batman Gambit. At first, it seem like he is content to use Kyurem's power to freeze Unova and force the population into submission. However, at the climax, when his son N (revealed to be the leader of Team Plasma's repentant splinter group that is opposing him) flies in to rescue the player on his Legendary Pokemon (either Zekrom or Reshiram, depending on the version) it is clear that not only did Ghestis expect this, he wanted it. He is then able to combine Kyurem and N's Pokemon into an even stronger version of Kyurem. Unfortunately, this plan is utterly ruined when Kyurem is defeated by the hero; while Ghestis is clearly the strongest boss up to this point, his sole reason for attacking the player is out of revenge.
In Eternal Darkness, the 100% twist ending reveals that the entire game was just an absolute brilliant gambit run by the guardian god Mantorok so that it could eliminate the Eldritch Abominations it was tasked with sealing before it died.
In Diablo II, the fallen archangel Izual reveals that :the Dark Exile, the capturing of the Prime Evils in soulstones and the plot of first Diablo was a Batman Gambit planned by the Prime Evils and himself. This is no doubt a retcon, though.
This is taken to a whole new level in Diablo III, where the retcon goes a step further, revealing that even the defeat of the Lesser Evils and the Prime Evils in the previous game were all part of the plan to unite the collective power of all the Lords of Hell into one singular Soulstone as the "true Prime Evil", with Diablo's soul in control. And who was there to ensure it all went according to plan? Adria the Witch, an NPC from the first game. Retconning at its finest, turning the entire trilogy into one huge Batman Gambit
Laharl uses one in Episode 6 of Disgaea to lure all of his competitors for the Overlord's throne into Blair Forest, set up as a contest to wrest the "Deed to the Title of Overlord" from him. There is, of course, no deed, and after a mild hiccup in the form of a Hopeless Boss Fight, Laharl and co. defeat their enemies, and he gets to claim what (he thinks) is rightfully his.
Also used a chapter earlier by his vassal Etna, who was supposedly the mole working for another deamon trying to overthrow Larhal. Only when he finally calls her onto the carpet she reveals that not only has she been expecting him to betray her, she's hired his own underlings out from under him, and set things up so that Laharl would be more than eager to help her take out Maderas.
Also in Disgaea: Hour of Darkness, the entire game is a Batman gambit on the part of King Krichevskoy and Seraph Lamington, using Larharl and Flonne to unite the netherworlds, and even using Volcanus' traitorous nature.
Mao's father (now a ghost) pulls off one of these in Disgaea 3: Absence of Justice by manipulating the Evil Plan of Big Bad Aurum against him. The gambit worked by utilizing Almaz and Raspberyl's good hearts to get Mao to open up his own heart. To help further that along, his hidden right hand man Champloo (he reveals his true allegiances and how he manages to be so good at investigation at the end of the game) to guide Almaz to be a proper hero.
The King of Town, of all people, manages to pull one off in Strong Bad's Cool Game for Attractive PeopleEpisode 2: Strong Badia the Free. The episode starts off with the King of Town placing Strong Bad under house arrest for not paying his new email tax: one Creamy Ding Snack Cake for every email sent or received, effective immediately and retroactively. Once Strong Bad breaks out, he launches into a massive screwball scheme to depose the King of Town, but as it turns out it was all a Batman Gambit the King of Town executed so that he could switch jobs with Strong Bad. The endgame involves turning the tables on the King of Town by levying an obscene tax against his precious snack cakes, inciting the King of Town to revolt against him and take his old job back.
Unfortunately, while it worked great in the game, the long-term consequences of it blew up in his face.
The entire plot of Ghost Trick hinges on a Batman Gambit set by Ray, a.k.a Missile from an alternate timeline to point Sissel in the right direction. Everything turns out according to plan, because he needed Sissel's Ghost Tricks and his ability to travel through phone lines; Missile-Prime couldn't prevent any of the deaths with his Ghost Swap power, nor could he travel through phones.
Mephiles, the Big Bad of Sonic the Hedgehog (2006), pulls one using Silver. He tells Silver that Sonic is the one who will destroy the future, counting on Silver being desperate enough to change the future that he'll jump on a chance to change it without questioning any of it.
In Soul Nomad & the World Eaters Rakasha travels with you, confident you will be able to defeat the other World Eaters (who he views as rivals), then waits until you are trapped and helpless before striking
In Half-Life 2 and especially Episode 2, it turns out that the G Man set up about everything that happened since the beginning of the first game. We still don't know what is hoped to be achieved with all this, though.
He appears to be operating by this scheme. He doesn't even hide the fact that he manipulates people into doing his dirty work for him but simply puts them into places and situations in which their personal goals will also help his plan along.
Some details make this a noteworthy example: short of magically discovering that the gambit exists, none of the Unwitting Pawns are even in a position to make it fail, and in fact, when one of them throws a Spanner in the Works that Shepherd is clearly not expecting or planning for, it actually ends up helping him anyway. This makes it seem like a Xanatos Gambit on the surface, but there is a failure condition that Shepherd would have no way of recovering from, and that's if the Russian's war against the United States had succeeded instead of being turned back.
God of War III revealed that the entire fucking series was a Batman Gambit designed by Athena so that she could gain the power of hope that she had in the first place but also kill all the other gods and destroy the world without implicating herself and become the one savior of mankind.
Kerrigan from Starcraft uses Batman Gambits frequently. She ends up getting the Protoss to work with her even after she's betrayed them repeatedly, mainly by manipulating and eventually abducting their Matriarch.
Duran is another user of this, manipulating Du Gaulle into killing his best friend, as well as using Kerrigan herself as an unknowing pawn in his scheme to create a Protos/Zerg hybrid.
Arcturas Mengsk is yet another possible example of this trope, getting Kerrigan and Jim Raynor to help him out and shelter him both before and after he's betrayed them on an epic scale.
In Star Wars: Knights of the Old Republic, one can pull this off against the two Sith masters of the Sith enclave on Korriban. When Yuthura comes to Revan to help her betray Uthar, you can agree to help her poison him. Revan can then turn around to Uthar, and tell him of Yuthara's plan. He will give Revan a device to help poison her. But then, the player can turn around and poison BOTH of them. Soon after finding the Star Map both Yuthara and Uthar stand there. After explaining some Sith lore, they suddenly open that they are now going to kill the other with Revan's help. It is then up to the player to decide who he wants to help, or he can even turn on both of them at once. Turning on both actually gives the player the ability to deliver an awesome "The Reason You Suck" Speech, detailing how you used both's ignorance and arrogance on each other to weaken both of them so they'd be easier to kill, and it was all because they had not properly plotted their own plan.
Knights Ofthe Old Republic II not only says this this was Revan's stock-in-trade, but shows you where Revan learned it by saddling you with Revan's former master, Kreia. Kreia openly pulls these on both Atton and Canderous to get them to join the party, and it's arguable she is pulling one on the Player Character as well, so that all of her enemies even the Force itself are left in defeat.
Neo-Geo game Cyber-Lip plays a Batman Gambit on the player. The game makes you think you're fighting against an alien threat, when you're actually helping the aliens by destroying the last human resistance, as the twist ending makes clear.
Turns out the plot of Borderlands and half of Borderlands 2 was one huge Batman Gambit. The Vault Hunters of the original game were tricked into opening the vault by Angel - the Mysterious face and voice that communicates with the party - so that Handsome Jack could take over Hyperion and rule the planet. The same thing happens to the Vault Hunters in Borderlands 2. They're tricked by Angel into destroying the defensive shields of the rebel group headquarters for Handsome Jack. Angel by the way is a Siren pretending to be a sentient AI and Handsome Jack's daughter.
Let's not overlook the hostage rescue mission which inverts this trope in Far Cry 3 where the protagonist helps the Rakyat warriors to ambush a slave trade convoy in Church Town, pursues the prisoner transport away from his fellow warriors, and catches up to the APC only to discover the first act's Big Bad waiting for him with a surprise knockout. Vaas relies on Jason Brody's newfound heroism to bring him out of safety where he can predictably be captured, just because Jason caught wind of people who needed help.
In DmC: Devil May Cry, Virgil reveals in the end that he was using both Dante and his human assistant and friend Kat to overthrow Mundus so he can take over and rule the human race in his place.
Yukari Yakumo from Touhou pulls one off in Silent Sinner in Blue. First off, she relies on Eirin to relay info back to the moon. Then she relies on Remilia to be greedy and try to take over the moon, distracting one of the two princesses. Then she tries to go to the moon, distracting the other. All the while Yuyuko and Youmu go through a backdoor she created while everyone with power on the moon is distracted. She then plays on the Lunarian's trust of those who are "pure" to keep Yuyuko and Youmu safe (Yuyuko and Youmu are "pure"). During the entire time Yuyuko and Youmu are on the moon she acts like she lost. The end result? A 1000 year old bottle of sake stolen by Yuyuko from under the noses of the princesses. Yukari declares victory afterwards.
Note that this is actually the FAILURE condition. Besides Remilia not taking the bait, the distraction failing, etc...Yukari had no control over Yuyuko, who was originally supposed to steal something of great value...Sake doesn't QUITE qualify.
Clive Barker's Undying: Jeremiah already became an undead years ago, and only called upon Patrick so he could kill off his siblings and Keisinger so nothing could stand in his way for his double-cross. Said double-cross is followed by an Idiot Ball and a Shaggy Dog Story when it turns out that (A) Patrick CAN kill Jeremiah in one hit, which he does with glee, and (B) Jeremiah's ultimate goal, the power of the Celtic's Undead King, was a Barrier Maiden to an Eldritch Abomination that threatens both living and undead.
Tears to Tiara 2: Izebel's plan for the Tartetos campaign. She would send two forces to raze the town of Tamar: Laelius would take her own elite Hispanic contingents. Without informing Laelius, a separate force made of golems and monsters sent as reinforcements from The Empire would take a separate route. Hamil would sally forth from Tartetos in order to save the villagers at Tamar. Already angry at being ordered to massacre innocent civilians, on learning about the second force Laelius would defect to Hamil so that Tamar would quickly be saved. The action at Tamar would leave Tartetos wide open to a naval attack by portage, resulting in a Decisive Battle that would see the imperial army from the empire proper wiped out and she herself die by Hamil's blade. It requires both Hamil and Laelius to act exactly as she planned. And they do, because they both believe very strongly in protecting the innocent. And in the case of Hamil because he told her all his battle plans when he was a young child before he lost his memories.
DuckTales Remastered reveals that the entire treasure hunting adventure was a plot by Magica DeSpell in order to obtain the pieces needed to resurrect Dracula Duck. She knew Scrooge McDuck would buy the portrait of Dracula Duck for an incredibly cheap price, discover the map and go hunting down the treasures.
Fallout 4 has one, where Father uses Synth!Shaun to implant a memory into Kellogg, knowing that the Sole Survivor would be looking for a way into the Institute and would have revenge on the mind after coming out of the Vault.