In the final case of Phoenix Wright: Ace Attorney - Justice for All, Phoenix must decide between saving Maya from an assassin who's holding her ransom to force you to get an innocent verdict for his guilty client, and condemn an innocent to take the fall for the murder, or to expose his client as guilty but let Maya die. In the end, he manages to convince the assassin to drop his contract and release Maya by showing him that that his client had planned to betray him all along; once he realizes that his code of honor and confidentiality was used against him, he announces that he won't rest until the man who duped him is dead, who immediately becomes so scared for his life that he begs for a guilty verdict so he'll be safer inside jail.
There are also multiple points where the Player Character reconciles a contradiction by saying that the contradiction itself is true. The most notable is in the final case of Trials and Tribulations when Iris appears to be in two places at once according to two separate pieces of testimony. Which testimony is true? Both. One of the 'Irises' is her twin sister Dahlia, being channeled by Misty Fey.
In Gyakuten Kenji 2, Edgeworth is asked whether he wants to uphold the law as a prosecutor or to save people as a defense attorney. By the end of the game, he decides to save people as a prosecutor.
Phoenix Wright: Ace Attorney Spirit of Justice has a massive one near the end; Apollo has to choose between trying to apprehend the Big Bad (which will result into an innocent being also condemned to death due to the local laws)note The innocent in question was blackmailed by said Big Bad into giving a false confession and taking the blame for the Big Bad's crime; however, the Defense Culpability Act law makes it so that, if someone is condemned for a crime, then anyone who aided them in the same crime will receive the same penalty as them. or letting the Big Bad go scot-free. Additionally, the Big Bad in question is the Queen of Khura'in, and she has used her royal authority to emit new laws during the trial she's in so that she doesn't get convicted. In the very end, Apollo realizes that the reason the Queen kept searching for the Founder's Orb throughout the entire game is because she doesn't have spiritual powers (something that a royal absolutely must have if they want to claim rights on the throne of Khura'in). He then challenges the Queen to channel the Holy Mother; when she fails, she's not only dethroned but every single law she ever made was rendered invalid because it was made by an illegitimate ruler.
For a Rogue-alike, ADOM has an unusual amount of plot, and there are several Third Options available in the game. If you take the quest to look for the village carpenter, you'll find he's become a dangerous Chaos monster, who will attack you on sight. It's kill or be killed ... or you can lead him to the healer Jharod, who will fix his corruption and teach you the Healing skill as a reward. Later on, you'll meet an undead dwarven warrior, who can be defeated by force, or destroyed instantly by pouring holy water on his grave. Later still, you'll run into a dying sage who can't be healed by any normal spells, but he won't move off the stairs to the next level until you talk to him, at which point he dies. The third option is to give him an amulet of life saving. When it comes to the endgame, you can close the Chaos gate and kill all the monsters on the level, preventing it from being reopened ... or destroy the levers so the gate can't be reopened ... but if you've done a variety of difficult tasks, you can go through the gate instead and fight the god of Chaos for a special ending.
Antichamber: Many of the puzzles will have this as a solution. Early on there is a hall leading to two stairways, one going up and one going down. It doesn't matter which one you take, they both lead back to right in front of both stairways, the solution is to turn around and go back down the hallway you came.
Getting the best endings of all three games in the Ar tonelico trilogy boil down to this as the main heroes are constantly getting pulled into the actions between two major factions that are trying to save/change the world their own way (and have to be helped/stopped at one point or another) but, in the end, find their own solution that benefits everyone in the end.
In Atelier Lulua: The Scion of Arland, Lulua is faced with a cruel choice at the end of chapter 9: The Fellsgalaxen ruins have become so severely damaged that they could collapse at any moment, which would lead to the total destruction of the Arklys region. The only way to fix them is to use Fellsgalaxen's self-repair system, which would require Stia to sacrifice herself to activate it. The game doesn't give you the choice to allow your hometown to be destroyed, but you can also choose to reject both possibilities (and are required to do so to avoid the bad ending): by creating a Memory Core, Lulua creates a backup of Stia's consciousness, and once the repair process is done, she can forcibly remove Stia from the device and re-upload her mind into her body.
Throughout The Awakened Fate Ultimatum, you are asked to have your playable character, Shin Kamikaze, make either the "angelic choice" or the "demonic choice." At the end of the game, you have to choose whether to save the angel Jupiel or the devil Ariael. Once you have saved one of them, however, and seen the credits, you can save and then load from the save file to go back to the choice. This time, you have a new option, "I'll save them both, no matter what." This is the way to see the game's true ending.
Since Baldur's Gate is a BioWare series, there were bound to be some of these, whether used in the original game or added through mods.
In the extensive Baldur's Gate NPC mod, there are three romantic suitors for a female PC. Two of them, a knight and a rogue, will go through a series of impressive challenges in the hope of winning the PC's heart, which may well make it very difficult to decide between the two. Since the third opts out due to thinking his chances are hopeless, this makes him an endearing and tempting third option (as evidenced by polls, wherein he is the single most popular choice of either gender.)
Early on, the PC is given a (theoretical) moral quandary similar to Morton's Fork, involving the PC and his (imaginary) sister being trapped in cages by a wizard and each having to choose whether to try to save themselves or their sibling in a variant on the Prisoner's Dilemma. If Minsc is in the party, he interjects by saying that he would smash open the cage and attack the wizard for playing such a trick.
Later, the Player Character and his/her party are infiltrating the drow city of Ust Natha, in an attempt to retrieve a good dragon's eggs. Two of your bosses are Matron Mother Ardulace and her daughter Phaere. When Phaere reveals her plan to supplant her mother, you can choose to go along with it or betray Phaere to Ardulace. Since both people are nasty pieces of work, the only difference between the two decisions is the amount of Experience Points you will receive. In either case, the dragon's eggs will likely end up tainted as well, scuttling your mission. However, if you chose not to kill Phaere's ex-lover Solaufein, he gives you a way to betray both of them, saving the eggs and giving both Phaere and Ardulace a spectacular dose of Laser-Guided Karma.
A sidequest involves encountering a woman being held for ransom. The reward for the ransom turns out to be a unique object required for unlocking an extremely powerful item late in the game. The player can choose to free the woman or meet the ransom payer and pose as the kidnappers, netting the valuable object at a significant hit to their reputation. Or, if the player is particularly smart, they can pickpocket the item off of the ransom payer, then slip away without a word and return to the woman to set her free. The woman actually acknowledges that you left her to rot and is rather pissed but because you are ultimately letting her go she drops the issue and the player does not suffer reputation loss.
The turning point of Makoto's story in BlazBlue: Continuum Shift has her pinned under a Sadistic Choice - Relius has taken off with Jin Kisaragi, but Noel and Tsubaki are still out there and unaccounted for, with Hazama having nobody's best interests at heart. If she chooses to go after Jin, she winds up running into Relius; if she chooses to go after Noel and Tsubaki, Relius could catch up to her. Either way, the situation had to be resolved, and quickly, lest someone wind up dead. The best option is to go after Noel and Tsubaki anyway; as it turns out, Makoto thought ahead and asks Bang to round up Jin in her place, leaving Relius preoccupied while she deals with Tsubaki. Not only does Relius lose sight of her and Jin, but by the time Hazama catches up to Tsubaki, Makoto has gotten hold of her and renewed her spirits, leaving his plans in utter ruin and his patience stretched beyond its threshold. Rachel is along to retrieve Makoto soon after.
This is taken one step further in the Full Body version, which introduces Qatherine/"Rin" as a Third-Option Love Interest. Technically, she's the fourth option if you factor in the Freedom route, but still. Rin isn't directly involved with the main love triangle. She's suffering from amnesia, just wants to play the piano, and make people happy. She's sweet, earnest, supportive, naive, and completely harmless. Rin is actually from a race of shapeshifting Angelic Aliens whose human form is that of androgynous male. The other women barely notice her, and even the Big Bad doesn't see them as a threat despite knowing their true nature. She's open-minded and has some unusual - but profound - ideals: No one can tell someone else how to live their life, and that individuals are the only ones should decide what is important to them. If you choose to romance Rin, this philosophy turns out to be exactly what Vincent needs to hear to take a step back from the whole Katherine/Catherine debacle and reassess his life. Not only does Vincent become a far stronger, more competent person, he realizes Rin makes him happy and that gender doesn't matter to him. This completely derails Catherine's strategy, because she doesn't realize Rin is a factor until it's too late, and the likelihood that Vincent has been bisexual the entire time. Rin's piano playing also has the power to slow down the Big Bad's Nightmares, and grants any listeners the ability to see new possibilities and opportunities. In that sense, Rin's greatest trait is the ability to help people Take a Third Option.
In the endgame of Close Your Eyes, you have the options of joining the Husks and freeing them (Husk Ending), giving the Witch her other eye (Recollection Ending), or you could wait until the timer ticks down and watch the V.I.E.W facility explode (which takes you to the Best Ending).
In Dark Souls you are presented a fairly binary choice at the end of the game after killing Gwyn in the Kiln of the First Flame; either you can choose to Link the Fire once more which results in you immolating yourself to allow your souls and Humanity to fuel the fire or you can choose to Abandon the Fire which sets you up as the Lord of the Age Of Dark, which if Artorias of the Abyss is to be believed is gonna seriously fuck up the world. However, this binary choice sets the stage for a third option to be considered
In Dark Souls II, where the knowledge that the act of Linking the Flame or letting it fade is not two choices, but one that serves to perpetuate an endless cycle of Light and Dark that constantly ebbs and flows between the two. King Vendrick and his brother Aldia attempted many experiments to try and cure the Undead Curse without giving into the cycle, but wound up becoming a deconstruction of trying to find a third way out as opposed to taking one bad option and sticking to it; Vendrick was being sabatoged from the start by Nashandra who wanted the power of the First Flame for herself and wound up contracting the Curse and hollowing out in the Undead Crypt, and while Aldia did break himself out of the cycle of the Curse, doing so wound up costing him everything that made him human and turned him into a plant-like Eldritch Abomination with no souls and Complete Immortality. When you encounter Aldia he even states that the solution he and Vendrick came up with (harnessing the First Flame and the Dark Soul in tandem) is unattainable because of how much one must sacrifice in order to do that. You can still choose to follow in Vendrick and Aldia's footsteps despite this, abandoning the Throne of Want to try and find a way out of the cycle on your own which is made infinitely easier since, by the time the option can be presented to you, you've essentially gotten a cure for the curse for yourself through the Crowns of Vendrick, the Sunken King of Shulva, the Old Iron King, and the Ivory King of Eleum Loyce, and thus setting the stage for
Dark Souls III, wherein the Fire has been linked and allowed to fade so many times over that the world is on the brink of complete collapse because it simply can't sustain it anymore. You as an Unkindled have the power of the vestiges of the Fire that can be emboldened through embers of the First Flame, making you the one being that can return the Lords Of Cinder to their thrones so you can attempt one final Linking of the Fire. However, the game makes no bones about how the world is going to die no matter what you do, you only get to choose how it does so; either you can Link the Fire one last time, honoring the sacrifice of the Lords before you and giving the world a last spurt of light and flame before everything fades away, or through giving eyes to the Firekeeper you can quietly snuff the First Flame out to allow a new flame, one untainted by the Linking and the Curse, to arise naturally from the Dark. However, there is a third option to be had through an obscure side quest that requires taking on Dark Sigils from Yoel of Londor, giving you the power to command the Dark Soul and the First Flame due to gaining Humanity from the sigils and your innate ability to embrace embers of the First Flame. Essentially, Vendrick had the right idea about how to end the cycle and the curse, he simply lacked the ability to take on the power of the First Flame the way that an Unkindled can. At the end of the quest line you absorb the last vestiges of the First Flame, combining them with your pieces of the Dark Soul to break the cycle of Light and Dark and take your place as the new Lord of Mankind, in what is either the best or worst ending to the game depending on your interpretation of the lore.
In Deus Ex early on in the game you are instructed by your CO to kill the unarmed leader of a group of terrorist/freedom fighters who has already surrendered or else she will kill him for you and report you for insubordination (which she will do if you try to leave or even so much as talk to him for too long). An unsaid, but also perfectly viable option, is to just kill her instead, and claim she got killed in the crossfire. It is difficult to do without killing the terrorist leader anyway because your CO explodes when you kill her.
It's possible: when you enter the terrorist's bedroom, put a LAM or two on the wall. After the first chunk of dialogue, when you hear Anna Navarre's footsteps, run to the bathroom, so you won't die too. When she's blown up, you can continue your conversation with Lebedev - it's worth it, for he has some crucial and interesting information.
Or you can take the fourth option, try for a non-lethal kill. It's impossible to actually knock out your CO, but you can do sufficient damage to cause her to run from you without landing the killing blow. You'll still be forced to kill your CO later in the game to move forward. Unless you take the third option again via sequence breaking. The game never adequately explains why your bosses seem to be unaware that you attacked your CO despite her being alive and perfectly capable of reporting the incident.
The Deus Ex: Human Revolution DLC "The Missing Link" confronts the player with a choice - poison gas is flooding the facility, and the protagonist can divert the gas to one of two areas, saving either hundreds of innocent people, or a whistleblower who is prepared to blow the horrific practices going on in the facility wide open. Finding and disabling the well-hidden pump for the gas nets the player high praise from some support characters and an achievement named "all of the above". You need to have the heavy-lifting and the jump Augs to achieve this, otherwise you are stuck to both of the Sadistic Choices.
In the main game you are faced with a bomb set to kill a set of hostages. You can find out the code from a terrorists PDA, hack into it and disarm it or you can just shoot it, shutting it down.
In the end of the first Dino Crisis, Regina must choose between helping a mortally wounded Gail (Regina's commanding officer) apprehend the renegade scientist Dr. Kirk, causing Gail to die in the process; or knock Gail out, forcing him to escape the island without capturing Dr. Kirk. The third option comes when the player chooses to knock out Gail, only to go after Dr. Kirk alone.
The game gives you a third option at Castle Redcliffe, where the Arl's son Connor has been possessed by a desire demon, torturing the castle denizens and wreaking havoc on the village with frequent attacks from the undead. At first the choices are to kill Connor or sacrifice his mother, Arlessa Isolde, in order for a mage to enter the Fade and slay the demon. But, if you ask about an alternative, you'll be presented with the option of having the mages of the Circle Tower assist in the ritual, sparing both. If you are a mage and choose to enter the Fade yourself, you're also presented with a second layer of this by the desire demon herself: Allow her to leave, temporarily relinquishing control over the boy, in exchange for a reward of your choosing, fight and destroy her, or if you've got enough skill in persuasion, intimidate her into leaving without a fight AND giving you the reward for not destroying her.
In the Dalish Elf quest, by the time you encounter the Lady of the Forest, she explains that the werewolves she protected were once humans, before the Dalish Keeper Zathrien turned them into werewolves, all as an act of revenge for his dead children. It's at that point that the player can either kill the werewolves and quench Zathrien's thirst for revenge, side with the werewolves and help them pay back the elves for their curse, or, as the ultimate third option, sacrifice Zathrien and the Lady of the Forest's lives to return the werewolves back into humans.
By the end of The Landsmeet quest, the Warden protagonist is given the option of killing the traitor, Teryn Loghain, or turning him into a Grey Warden while replacing Alistair with the teryn. He/she also has to decide whether Alistair or Anora becomes the new ruler of Ferelden. If Loghain is spared, Alistair can't be chosen to lead Ferelden. If Loghain dies, Alistair is a feasible choice for ruler of Ferelden. There is still a way to elect both Alistair and Anora as the new rulers of Ferelden, while Teryn Loghain lives and becomes a Grey Warden. First the player has to harden Alistair after the events of his own side-quest, so that he could be more willing to become king. After that, the player has to persuade Alistair and Anora to marry each other, so that both can rule Ferelden together, while Loghain lives. As a fourth option, if the protagonist is a human-noble, he/she can either marry Alistair if female, or Anora if male. Regardless of whom he/she marries, he/she becomes a ruler of Ferelden him/herself.
The ending also provides a third option. Instead of sacrificing yourself, or a comrade warden, to the Archdemon, you can have Morrigan impregnated, either by a male PC, or Alistair or Loghain. Doing this lets the Archdemon's essence join with the unborn child. And in an inversion, if Alistair is your love interest and you decided against performing Morrigan's ritual, Alistair takes away the option of sacrificing yourself.
Dragon Age II also subverts the idea that the third option has to be an optimal outcome in the quest Night Terrors. A boy with a rare magical talent is being threatened by demons. The choices first given to you are to either save him and let him run away to train his talents or to make him Tranquil (essentially a magical lobotomy). The third option is to let another demon posess his body, wreaking havoc with the boy's magical talent in exchange for a reward from the demon.
Dragon Age: Inquisition makes third options into a kind of a gameplay mechanic. As the title organization grows in influence, you gain access to "Inquisition Perks", among which are in-depth knowledge of the criminal underworld, nobility, magic, and Chantry history. Unlocking these perks adds secret third options to some dialogue trees, which are often more beneficial than the rest (such as making a captive Tevinter magister work for you if you have magic knowledge, instead of just executing him or arresting him).
Dragon Quest III: There are items and gear the Hero requires to successfully surmount certain obstacles, that Ortega overcame without. We'll never know the details, but it's obvious he found other alternatives that worked.
Dragon Quest VIIDeconstructs this with the subplot of Verdam/Greenthumb Gardens. Pepe finds himself faced with a Sadistic Choice: the woman he loves is engaged to the son of the richest man in town... who also employs his family as gardeners. Linda wants to be with him, but breaking the engagement would leave her family's debt unsettled and potentially threaten his family's livelihood; on the other hand, staying silent means having to watch her marry another man, and Iwan may still take his jealousy out on them... Under pressure, Pepe chooses to leave town entirely instead... but this winds up making matters worse, as everyone involved in the Love Dodecahedron winds up miserable.
In Duel Savior Destiny the Messiah upon ascending to their position is forced to choose between the Red Law (magic) and the White Law (science) to determine which will be the new natural law in the new universe. Taiga, who recognizes that both of them are necessary, chooses instead to beat up God and make him stop offering such shitty choices since they destroy the current universe.
The primary way of completing the main quest involves a lengthy series of quests in order to be recognized as the true Nerevarine of prophecy and accept a protective tool from one of the three Dunmeri Physical Gods that allows you to wield otherwise dangerous weapons that could kill you and use them to undo the antagonist's source of power. Alternately, or if you have killed any important people in your journey and "severed the thread of prophecy," you can take the "Backpath" approach by killing the said god Vivec and take the protective tool to last living Dwemer Yagrum Bagarn, who will "jury rig" it for you so you can still use it to safely hold said dangerous weapons that can kill you. The third option is an organic victory that involves either juggling the said dangerous weapons so they can't kill you while using them or using advanced alchemy to out-heal their deadly effect.
Two factions, Great House Hlaalu and the Fighters Guild, feature mostly corrupt leadership due to their being in the pocket of the Camonna Tong. Thankfully, each faction has a Reasonable Authority Figure (Crassius Curio and Percius Mercius, respectively,) who is working to rid the factions of corruption and aids the Player Character in doing just that. At points in each faction quest line, it is necessary to complete quests for the more corrupt members, usually with morally questionable implications. However, if you report to Curio or Mercius during the quest in question, they will usually offer an alternative, less morally reprehensible solution that still allows for completion of the quest.
A minor Game-Breaker for Oblivion, there is a quest for a daedra named Clavicus Vile to retrieve for him a sword called Umbra. If you do get the sword, you can either give it to him, for the reward of a crummymask, or you can keep it. The only problem is, while it's almost certainly the best sword in the game, it's also quite heavy. There is a third option; since quest items are weightless, Umbra has no weight value until you complete the quest. Therefore, by simply not ever finishing the quest, you make it into what is VERY DEFINITELY the best sword in the game: superpowerful and light as a feather- and capable of eating the souls of those it kills.
If you start looking into the Dark Brotherhood in Skyrim, you'll find yourself waking up in a locked shack, where the Brotherhood's chief assassin explains that you owe her group one murder. She has three bound and hooded victims waiting for you - a harridan of a housewife, a blubbering Nord mercenary, and a Khajiit who unrepentantly mentions that he's a rapist and murderer - and explains that there's a contract on one of them. Someonehas to die before you leave the shack. Kill one and the assassin will welcome you as an initiate in the Dark Brotherhood. Kill more than one and she'll praise you for your thoroughness. Or... you can kill the assassin (no easy feat), free the captives, and report to a city guard, starting the "Destroy the Dark Brotherhood" quest in which you assault the assassins' lair and wipe them out for good. This is an improvement from Oblivion, where you could only opt in or out of the Brotherhood without doing anything else.
During the quest ''No One Escapes Cidnha Mine", your initial option is to side with Madenach and escape from the titular mine and then kill Thonvar Silver-Blood (which gives you the unique Armor of the Old Gods), although you can also kill Madenach and use his escape plan (which has Thonvar give you his family ring). However, the game doesn't force you to stick with Madenach the whole way through, meaning there's nothing stopping you from siding with him to escape up until you get the armor, then killing him immediately afterwards, which has Thonvar act as if you killed Madenach before escaping and causes him to pardon you and give you his ring.
In the series' backstory, the Tsaesci are an Akaviri race of supposed "Snake Vampires". However, sources conflict greatly over whether they are indeed serpentine or are humans not all that different from those in Tamriel. A third explanation states that since the "races" of Akavir share their names with the name of their nation, it's possible that they aren't one single "race," but multiple races living within those nations. The "Tsaesci" could include serpentine snake vampires as well as the former Men of Akavir and/or their cross bred descendants.
Also from the backstory, the ancient Falmer (Snow Elves) were faced with a Sadistic Choice - extermination at the hands of Ysgramor and his 500 Companions or accept the terms of their Dwemer cousins for protection, which included blindness, enslavement, and mutation (both of the physical variety and of their very souls). While most of the Falmer race chose the latter option, a small population was able to survive in hiding at the extremely remote Chantry of Auri-El without the "aid" of the Dwemer.
Another backstory example - there is significant debate in-universe (and out) about the life of Tiber Septim, the founder of the Third Tamriellic Empire who ascended after his death as Talos, the Ninth Divine. Orthodox Imperial history states that he was born Talos Stormcrown, a Nord, in Atmora, and heroically rose to the position of Emperor of the first truly pan-Tamriellic Empire. Other sources, considered heretical, instead say that he was born Hjalti Early-Beard, a Breton, in High Rock. He was a shrewd politician and master manipulator who rode his many powerful friends to the title of Emperor and backstabbed them the moment it became convenient. However, a third option exists: The latter "heretical" story was true, but after his apotheosis, the deity Talos used his power to literally rewrite history, making the former true as well or instead. There is also kind of/sort of a fourth option relating to this: the Merger of Souls theory regarding Talos' ascension made the deeds of the multiple individuals who make up Talos all seem to have been done by one individual.
The third Exmortis game has one in the "Exodus" chapter. The Reader tells Mr. Hannay to choose between two doors. While either door will allow you to be with a deceased family member, entering either one dooms the earth to extinction. The correct decision is to use a nearby curtain rod to skewer the Reader.
After taking the throne, you discover why your brother Logan was such a terrible ruler, and you are faced with the same choice: either keep your promises to those to whom you have made them, thereby dooming Albion to the demonic presence looming on the horizon, or break your promises, gaining you enough funds with which to defend Albion from said evil. It's quite possible, though, for you to simply buy up all the property in the game, which eventually deposits enough money in the royal treasury for you to build up your defenses while keeping the moral high ground.
There's also an inversion in the early game where Logan forces you to choose between killing a group of protesting commoners and killing your childhood friend/lover. If you take too long to make this choice, he orders all of them to be executed.
In the main quest, good-aligned characters (and players) may have difficulty squaring themselves with the idea of running a raider empire, let alone picking which group of psychos they want as their best friend. No problem, there's a third option: wipe them all out.
Dry Rock Gulch has an annoying set of fetch quests given out by robots. Generally, your only option is to do them - playing along with the game or grudgingly, your choice - unless you've leveled up your Robotics Expert perk, which will allow you to just enable an override in the bots and skip the whole time-sink mess.
Rather than just choosing to side with the NCR or Caesar's Legion, the Courier is given the choice to secure Vegas under the rule of Mr. House. You can even go one step further and decide to screw them all in order to make Vegas an Independent city-state under your own rule with the help of the Yes-Man A.I. Additionally, in many more minor choices the player has to make they can sometimes, if they have enough of the right skill, choose an extra option (it's also there when they don't have the skill, but it has no effect and both the player's words and the response are generally Played for Laughs) that will reward them with a sense of satisfaction, some amusing or badass dialogue and will often allow them to skip an annoying resource-gathering quest or give them the advantage of free or cheaper weapons, armour or supplies.
There is one case where not having enough skill but still choosing the skill-option opens up a new option: in the final battle against Lanius, if you fail the final skill check in the chain to convince him to retreat, a less hard speech check becomes available: talking him into fighting you one-on-one.
Chrom and Lissa's sister Emmeryn, the Exalt/Queen of Ylisse, is captured by the Plegian army and made to stand atop of a cliff to force her heir Chrom into a Sadistic Choice: either he hands the Fire Emblem to Plegia (which will trigger the ruin of the continent) or they will kill her in front of him (which will seriously cripple the leadership of Ylisse as a whole). Emmeryn's choice? She gives a brief Rousing Speech... and then willingly throws herself off the cliff.
Another one takes place in Virion and Olivia's supports. He's teaching her some new dances but one of them is a duet, and she's too shy to go through it. Will Virion step on Olivia's boundaries so she'll learn new dancing steps, or wil he stop the classes altogether/leave that particular one unfinished? He decides to go to the other side of the place they're both in and mimic the steps from that corner, so she can see the basics and learn them without problem.
This can be vital to the plot of Fire Emblem Fates. The Player Character can potentially reply to the choice between Hoshido and Nohr by siding with neither kingdom and becoming a fugitive with Azura, Lilith, and either Jakob (for a Female Avatar) or Felicia (for a Male one). This forces the armies to chase after him/her and their group instead... and unlocks the Revelation Third Path.
In the Nohr/Conquest path, the Avatar can take one in Chapter 23. Rather than killing Princess Hinoka (thus dooming him/herself emotionally and damage his/her reputation in Hoshido even more) or openly letting her go (thus risking the ire of King Garon and opening another can of worms), one can choose to have him/her take Hinoka's naginata as "proof" of her defeat/death, then secretly arrange for Hinoka and her group's escape. The deception is blown soon, but by that time Hinoka and Co. are already out of Nohrian reach.
Fire Emblem: Three Houses has you choosing a house to lead at the start of the game, with trailers revealing the houses will eventually go to war. There is, however, a hidden fourth option available to you if you follow one specific path but make a crucial choice right before the Time Skip: side with the Black Eagles, but refuse to support Edelgard when she reveals herself as the Flame Emperor. This loses you her, Hubert and the Death Knight, but gains you the ability to recruit Hilda and the Knights of Seiros, who wouldn't otherwise join the Black Eagles. However, this is Played With in that this "hidden" fourth option is actually the default route on the Black Eagles, with the player having to achieve several secondary conditions in order to even make the choice to support Edelgard after the Time Skip available.
FTL: Faster Than Light's random events often pitch a few choices with which to deal with the event, usually a safe option that yields little to no reward and an option that can potentially net rewards but risk hull damage, crew loss, an enemy Boarding Party, or a ship-to-ship battle. However, if you have certain weapons, augments, systems with sufficient upgrades, or races of crewmembers, the game may give you an option in blue text that lets you take advantage of what you have to take a lower- or even zero-risk action that will still net you rewards. For example, one event has a ship manned by Slugs, a race infamous for their underhanded schemes and tricks, with its crew asking you to investivate a supposedly-malfunctioning oxygen system. Normally, you can send your crew in, either discovering the Slugs staffing it are honest and get rewards for your generosity or end up dealing with Slug boarders after discovering they tricked you, or you can leave the ship be, gaining and losing nothing. If you have a Mantis crewmember, you can send them in, which guarantees that the Slugs will get trashed by the Mantis and forced to offer you rewards to make you leave them alone.
An infamous moment in video game history, in Final Fantasy VIII: when you are trying to acquire the Guardian Force Bahamut, you are asked several questions to test your character. The worst gag is the answer to the third question is an invisible third answer, which is only seen when you've decided on it.
The third option is a big plot point in Final Fantasy X: Between letting Sin continue its endless rampage against Spira, and sacrificing Yuna (and probably Tidus as well) in order to destroy it...only for it to inevitably come back anyway. The third option in this case was to take advantage of Sin's (i.e. Jecht's) weakness to the Hymn of the Fayth, then use the airship to get inside it, destroy it (him) from the inside, and use regular aeons and a good old-fashioned beatdown to destroy Yu Yevon (who created and controlled Sin) before he could recover. This was probably Auron's plan to begin with; he just let Tidus and the others figure it out on their own.
In Final Fantasy X-2, Spira faces a dilemma over what to do with the ruined city of Zanarkand. Tourists want to visit it, because it's beautiful and teaches them about Spira's long-censored past. Traditionalists see it as a sacred place that should not be disturbed- especially for profit, because that disrespects all the people who died when Bevelle slaughtered the city. In the Golden Ending, these sides reach a compromise: people are going to live in Zanarkand permanently. They'll still get to enjoy it, but it will be honoured as a home instead of used as a tourist attraction.
Final Fantasy Tactics sort of has one. Near the end of Chapter One, Tietra - the sister of Delita, Ramza's best friend - is taken hostage by the Corpse Brigade (long story short, they mistook her for a noble along with Alma, her best friend and Ramza's own sister, and she was the one unlucky enough to be abducted successfully). The kidnapper, Golgorath, holds a knife to her throat when Zalbaag and his forces catch up, and threatens a choice - let him go free and live, or he'll kill her. He's actually hoping for the former, but is willing to spite them. As Ramza and Delita arrive, Zalbaag makes a horrific Third Option: order Argath to Shoot the Hostage instead and then Golgorath afterwards. Technically speaking this resembles Option #2, but with a twist - Zalbaag is refusing to comply with either alternative and would rather not let a rebellious criminal (albeit one with sympathetic motives) dictate his options. Ramza does call him out on this much later in the plot, too.
Geneforge 4 has you start off allied with rebels who will kill thousands to overthrow the government, but will let you defect to the other side, which will smash the rebellion and reinstate oppression and servitude. Both refer with distaste to some group known as the "Trakovites," which they're doing their best to stamp out...
In Genshin Impact, Diluc makes his contempt for the Fatui very clear, saying that if he were given the choice of joining them or eating a live Cryo Slime, he'd prefer to be crushed by a meteorite.
Grand Theft Auto: Vice City exemplifies the whole concept of sufficiently advanced video games allowing a third option. One mission has you chasing a crazed stalker. The official game guide suggests ramming his car until it explodes or doing a drive-by. It's possible to steal enough cars to create a roadblock and then use the rocket launcher. This is just one of dozens of examples.
At the climax of Grand Theft Auto V Franklin is offered two options: kill his friend Michael for Merryweather Security owner Devin Weston, or kill his friend Trevor for high level FIB agent Steve Haines. Weston refers to defying both of them as "Option C" and a death wish. If you choose "Option C" (which is the option Franklin alludes by insulting Devin), Franklin, Michael, and Trevor take out Steve, Devin, the leader of the Triads that's been harassing them, and Stretch, the guy that has been getting Franklin's friend Lamar into trouble, for goodmeasure.
Devin: So are you gonna, A. Listen to some fifty grand a year pension hunter, or B. A billionaire? who even the president lets finger his wife, or C? Try and be really stupid and save those two idiot mentors of yours and have everybody in the goddamn state crawling up your ass, A, B or C? Time's ticking pal, beep, beep, beep and your answer is? Franklin: Man, you know what? (opens door) Man, fuck you. Devin:Genius answer, pal. Total genius, but time is running. You think about it. Me? I got a triathlon coming up, and I am in deep training. Buh-bye! (leaves) Franklin: Man, fuck you! (slams the door closed before mission selection)
When you examine the Magicant machine in The Halloween Hack, you are given two choices: "Kill the monster" and the text box border (which the game tells you to pick a "real answer"). To see the rest of the game, you must refuse by pressing the B-button.
Halo: Combat Evolved: The Flood have been released, and the apparent options are to either let them spread and consume everything in the galaxy, or activate the Halo, wiping out the Flood... along with any living thing sentient enough to be infected by Flood. Cortana comes up with another plan; Chief destroys the Halo, eradicating the Flood and preventing galactic destruction.
In Jade Empire, instead of (Good Ending) healing the water dragon or (Evil Ending) claiming her power for yourself, you can sacrifice yourself and let Master Li win. Your reward for allowing his evil dictatorship? A statue of yourself. Derp.
In Kingdom Hearts: Chain of Memories, after playing through the game as Riku, Riku meets up with King Mickey, who suggests that he keep his dark powers, saying something to the effect of, "You chose a road I never even thought of; I want to see where that road leads." Later, when asked whether he'll take the road to light or the one to darkness, he takes the one in the middle... "the road to dawn."
Technically, this is a fourth option. The first two are the aforementioned roads to light and darkness; when Riku says that he is taking the middle road, DiZ asks whether he is taking "the twilight road to nightfall." Riku replies with his choice of the road to dawn.
In Kingdom Hearts II, the villain Xaldin of Organization XIII has the Beast caught between a Sadistic Choice. He has stolen the Beast's rose, as well as Belle. However, he will let one of them go, at Beast's choice. And there's not a damn thing Beast can do about it. Belle, on the other hand, catches Xaldin off guard by elbowing him in the side, takes the rose, and runs. Even Sora notes that as Belle's running, she seemed to be having a really good time.
In The Strange Leaflet Quest, a giant presents you with two goblets of potion; he says he'll reward you if you pick the right goblet, and the wrong goblet will poison you. Both goblets are poison; the correct response is to use the CLEESH spell which turns the giant into a newt.
A third example in the undersea area: A turf war is being fought between two gangs of fish obsessed with sport: the Ice Skates and the Roller Skates. You can help one side against the other, or help a third faction, the Skate Board, drive both away.
Legacy of Kain: Soul Reaver 2 sees (and deals with the results) of this exchange:
Raziel: You said it yourself, Kain — there are only two sides to your coin. Kain: Apparently so. But suppose you throw a coin enough times... suppose one day, it lands on its edge.
The above was due to a choice Kain had to make. If he killed himself, it would seemingly restore the pillars of Nosgoth, but that would finish off the vampires. If he didn't kill himself, then the vampires would remain due to his presence, but Nosgoth would remain. At first it seems he chose option two out of a desire to survive. It turns out that the entire situation was crafted carefully by Moebius and his Elder God. If he killed himself, Nosgoth would be doomed anyway because the vampires kept the pillars preserved. He actually took a third option. In a convoluted (but awesome) scenario he purified himself so he could fulfill his destiny as the Scion of Balance, making the pillars unnecessary.
Soul Reaver is one big quest for that 3rd option which will satisfy everyone who hated the end choices from Blood Omen: Save the world but sacrifice yourself, or rule over a crumbling Nosgoth.
In the second quest of the original The Legend of Zelda, some dungeons will contain old men that will seal you in the room and force you either pay 50 rupees or sacrifice a Heart Container in order to proceed. Players can also choose to attack the old man so the torches launch fireballs at Link until he dies and then restart at the dungeon entrance with both rupees and hearts intact.
The Legend of Zelda: A Link Between Worlds: This is what the entire ending is. Lorule's Triforce was destroyed long ago, dooming the world to decay and destruction. Hilda (the Lorule equivalent of Zelda) masterminded the entire scheme to steal Hyrule's Triforce to save their world. There seem to be 2 choices: give up the Triforce to Lorule so it can be saved (dooming Hyrule to decay and destruction), or leaving the Triforce in Hyrule, dooming Lorule to decay and destruction. Ravio (the Lorule equivalent of Link) says that there has to be another way and convinces Hilda to not destroy another world to save theirs. After she sends Zelda and Link home, they make a wish on their Triforce to restore Lorule's Triforce, saving both worlds.
This is needed to get the best ending in Lunarosse. Noel is dead, seemingly preventing anyone from going back to the real world instead of the one they're trapped in, and the armies of Corlia and Yliandra are about to go all out on each other for all the marbles. Garret offers the party the choice of which to aid and rule over Lunarosse. If you recruited all possible party members (Zelda and Izumi don't count), you can choose to have Channing reject both sides, point out how stupid their continually backing either side has been so far and vow to find a way back home. This sets you up on the path to finding that way.
In Mass Effect 2, Tali's loyalty mission involves being her being accused of treason. While investigating a quarian science ship, Shepard finds evidence that Tali's father was conducting dangerous experiments on the geth. Shepard can choose not to tell the quarians about this, which is what Tali wants. This results in Tali's exile, but earns her loyalty. Shepard can also reveal the evidence, which gets Tali acquitted but loses her loyalty. Or Shepard can call out the quarian admirals for their politicking and shame them into acquitting Tali while still earning her loyalty. There's also a fourth option here, or a second third option, as it were. You can convince the other quarians you've encountered to stand up for Tali to the Admiralty Board, which has the same result as doing it yourself, but doesn't require the high Paragon/Renegade score that the first one does (and is a Moment of Awesome for them). You do have to make sure that they're alive and sane, though, and that's far from given.
The entire series is full of these, in the form of Charm/Intimidate checks. Most of them are "third options" that both do roughly the same things despite being tied to different karma, and that typically solve whatever problem needs to be solved without any trouble. This is why charisma is a good thing.
A good example is in Lair of the Shadow Broker: Tela Vasir is holding a random woman hostage, the normal options are to do as she says and drop all your ammo, shoot through the woman, or (with sufficiently high Paragon or Renegade) give either a Badass Boast or a "The Reason You Suck" Speech while Liara hits her with a table.
At the end of Priority: Rannoch in Mass Effect 3, Legion (or the Geth VI if Legion died in Mass Effect 2) tries to upload the Reaper upgrades into the geth, upon their freedom from the Reapers. However, the quarian fleet is still hellbent on obliterating the upgraded geth, causing it to be the one to be wiped out, instead. It's at that point, Shepard has to either continue the upload at the expense of destroying the quarians, or kill Legion so that the quarians can destroy their creations without getting wiped out themselves. The third option: use a reputation check to convince the quarians to stand down and allow the geth upload, which results in the two sides making peace and allying with the Alliance against the Reapers. This Golden Path has extremely steep requirements, only available if Shepard has at least four bars of Reputation, imported a Mass Effect 2 save where both Tali and Legion were recruited and survived, completed "Rannoch: Geth Fighter Squadrons," and did at least 5 points' worth of the following: destroyed the heretic geth in "Legion: A House Divided" (2 points), completed "Tali: Treason" by using a reputation check to get Tali acquitted without giving evidence of her father's treason (2 points), brokered an agreement between Tali and Legion in their argument (1 point), and completed "Rannoch: Admiral Koris" (1 point) by rescuing the admiral instead of his crew (1 point, separate from the other).
The ending of the third game plays out this way. There's two regular options that are suggested by Admiral Anderson and the Illusive Man respectively, destroying all the Reapers (and all synthetics by extension) or controlling the Reapers and ordering them to leave. However, if your Effective Military Strength score is high enough, the Catalyst provides a third option of combining synthetics and organics, ending the cycle of synthetics vs. organics. As of June 26, 2012, the Extended Cut adds a fourth option, killing off everyone in the galaxy. However, the after-credits scene indicates that the next cycle was able to defeat the Reapers using the information in Liara's beacons.
Specifically averted for the Virmire scenario in the first game. Originally it was planned that, with the right choices, the player could save both Kaidan and Ashley. However, the developers realized that doing this would make that option the "right" option, which would defeat the point of the scene, and removed it.
In Myst, you're presented at the start with brothers Sirrus and Achenar trapped in books, each accusing the other of destroying their father's books and being wrongfully imprisoned by said father. Additionally, Achenar claims that Sirrus killed their father, while Sirrus says that father went on a journey to discover the truth and was never seen again. Throughout the game, you collect pages that allow you to hear more of the brothers' stories (while finding virtually no evidence that would support either of them). In the end, you're confronted with the choice between freeing Sirrus or Achenar. The correct answer: They were both in on it, and you shouldn't free either or you'll be trapped yourself. Instead, you have to use the green book which both brothers warned you against, freeing their father to destroy the red and blue books. Oh, and make sure you take the right third option, i.e. get the white page before using the green book.
The whole series has many problems like this (as well as many puzzles in which you just have to solve it the long way). For example, in Riven, Gehn gives you the option of using the Trap Book (which he thinks is a Linking Book that will take him home), or of refusing, which will get you killed if you do it too many times. The solution is to voluntarily use the book and trap yourself, which will convince Gehn to use it as well, thereby taking your place in the Trap and freeing you.
Myst III: Exile offers such a dilemma. Once you've activated both of the crystal podiums in Narayan, Saavedro will approach you and, realizing that the Narayan society is still alive and well and that he can't go home without you turning the outer shield off once he's on the plaform, will tell you to release the outer crystal and will walk out. Refuse and he'll eventually kill you. Do as he asks, and he'll gleefully toss the Releeshahn book into the drink and ride off, leaving you to go back to Atrus empty-handed. The best answer? Turn off the power, trapping Saavedro between the crystals. If you approach the window after doing it, he'll give you the Releeshahn book and will plead for you not to leave him trapped. This leads to yet another of the same type of dilemma. If you leave him, Atrus will comment on the cruelty of that act, but if you turn the power back on, lowering the inner crystal, he'll charge back in and kill you. The answer this time is to turn the switch lever and then restore power, releasing the outer crystal and allowing Saavedro to return to his home without ever exposing yourself to him.
In Myst IV: Revelation, you're confronted with Yeesha strapped to a chair, asking to be freed by pulling a silver-colored lever. Her brother Achenar is also in the room, and claims that Yeesha is actually Sirrus, his brother, transferred into her body, and demands that you pull the amber-colored lever instead. Taking a third option by refusing to act is not the correct solution in this case (subverting the trope); in fact, this is one of two ways to get a bad ending (the other one is pulling the silver lever). The correct choice is to trust Achenar and pull the amber lever, which transfers Sirrus out of Yeesha's body.
Finally, in Myst V: End of Ages, the player is constantly running into Yeesha and Escher, who each cajole you in different ways to give the Tablet to them, but who are each unworthy to have it for different reasons. The answer is to put the Tablet on the ground, so that it can be picked up by the Bahro, who were its rightful owners originally.
In Mario & Luigi: Partners in Time, when the titular Bros. try to access the Star Shrine, the Sprite gives a test of purity. Examining Mario's spirit, the Sprite determines that he is pure enough (and mildly overweight, at that), but Luigi's past is dark enough (eliciting some horrified mutterings from the Sprite) to bar him from entering, and he must hit a special block in order to get in. After completing the puzzle to get the block to the door, Luigi is unable to hit it, and the Sprite asks who was responsible, giving you three choices: 1) Mario, 2) The Babies, 3) Luigi the correct answer is 4). After taking the test, the Sprite is dissatisfied with Luigi's dishonesty and agrees to only let Mario and the babies in, ignoring the point-out that he only gave three answers, none of which were correct. Mario debates on Luigi's behalf to the outraged Sprite, and his selflessness is apparently strong enough for both of them. He then reveals that the whole event was a test in and of itself, and they passed with flying colours.
In some instances where two members of the party have conflicting strategies, you have the power to either side with one of them or present an entirely new idea.
In the first episode, when discussing what to build in front of your fireworks display, Olivia will suggest an Enderman while Axel will suggest a Creeper. You can agree with one of them, pick a Zombie or say nothing.
In The Curse of Monkey Island, Guybrush Threepwood is asked, while challenging a pirate to a duel, to "Choose your weapon," and is presented with a case full of pistols. No matter the weapon he chooses, he loses the duel. If the player closes the case, a banjo is revealed to be behind it. The correct option is to choose dueling with banjos. Then, when the other pirate proves to be a truly incredible banjo player in addition to a crack shot, pick up a gun and shoot the banjo, proving that Guybrush is an underhanded cheat- and thus, a true pirate.
In Mortal Kombat 11's Story Mode, Raiden is forced to fight Revenant Liu Kang. The Revenant absorbed his past self's soul, which means that, if he dies, his past uncorrupted counterpart dies too; and on top of that, the only way that Kronika can be defeated is if Raiden and Liu Kang ally themselves against her. So, if either Raiden or Liu Kang die, Kronika wins. Raiden comes up with a solution: fusing with Revenant Liu Kang, thus making him a god. Since there cannot be two versions of the same god in the same timeline, Revenant Liu Kang gets replaced by past Liu Kang, with his soul restored, fully uncorrupted, and possessing Raiden's powers (including his godly resistance against Kronika's time powers) plus the Revenant's memories (including knowledge of Kronika's plans).
The Merged Reality of no-one has to die. When the visitor (I.E you) gets all four security codes, there is no need to choose anymore; all four of the people can escape the fire.
Played straight in Neverwinter Nights. When you reach the village of Charwood, you are told to affix the blame for a centuries-old massacre. It turns out that the murderer was neither of the adversaries responsible for half the events, but rather the demon that was manipulating them both. On the other hand, exposing the demon leaves you in another dilemma; you can either let a demon lord go free and bag yourself a magical trinket, or doom a town of people to eternity in amnesia and madness in order to trap the balor. Great, huh?
Even after revealing the demon lord you can still decide if one of the former suspects is guilty. One of the suspects could have chosen not to execute the massacre and abandoning his plan with eternal undead. The overall outcome is more positive.
A note from a speedrunner of the game: there's actually a sixth option here. You're here to get a journal that contains information, right? What has that got to do with solving a murder? Most people assume that the video game logic of cause and effect is here complete the area, get the reward for continuing even if it's apparently unconnected but although solving the murder does indeed point you to the journal, the game is more realistic than that, and you can genuinely just search for the journal and take it without ever investigating the murder at all.
Aigis of Persona 3 FES has to make a tough choice - leave behind the memories of the person she loved, or go back in time to save him (which would doom humanity or get them stuck in their dormitory forever). Instead she decides to find out how exactly the Main Character performed his miracle and if there's a way to save him using the last remaining Door of Time, which allows them to use the Key of Time for something else, like leaving the dorm.
In the MMORPG PlaneShift getting killed sends you to the Death Realm, which you have to explore to find the portal leading back to the mortal coil. Your first choice comes when the bridge you're on branches. Right or left? Both paths are dead ends, just keep going straight ahead and drop off the bridge.
In Pokémon Platinum, Cyrus tells you that whether you defeat or capture Giratina, its rage will destroy the universe and let him recreate it. Cynthia tells you (rightly) that he's lying, but even she says that you have to fight Giratina. However, once the battle begins, you can escape it like any other wild Pokémon encounter. If you do so, Cyrus exclaims that he didn't expect you to back down, much less that doing so would actually satisfy Giratina.
In Pokémon Sun and Moon, to get the Ride Pager number for Grimsley's Sharpedo, you have to correctly call his coin flip: heads or tails? You'll be right regardless, but if you select "Neither" he's surprised and admits he was going to call on Skarmory to steal the coin in mid-air.
Not doing anything during the "Live Selection" sequences of Resident Evil 3: Nemesis is a third potential choice along with the two given. If monsters are involved it simply leaves you to your devices to kill them, but in other cases sometimes an entirely different outcome instead of the two choices can happen. Including a third potential ending sequence.
One was taken by Sougetsu Kazama in Samurai Shodown III. Faking your rebellious little brother Kazuki's death so he and your sister Hazuki can run away is way more useful than either letting him go and being marked as a failure by your clan, or killing him and definitely losing both of your siblings.
As the main character, you get to choose between two delightful extremist philosophies: Law (Usually represented by the Messians who prize blind obedience and worship YHVH, a vain dictator who created the world to be his) or Chaos (Usually represented by the Gaeans, who support a state of violent anarchy in which it's every man for himself, and are usually aided by Lucifer). Seems it's only logical to think that the correct answer to this conundrum is to say "Screw you both! The two of you are INSANE!" and choose Neutral, which supports personal liberties and individuality while having enough law and structure as to not fall into a state of anarchy. It's idealistic, sure, but Law and Chaos do have some things going for them, and by opposing both sides, you make God and Lucifer hate your guts. The end result is usually Omnicidal Neutral.
In Shin Megami Tensei I, American ambassador Thorman (Law) declares martial law in Tokyo when demons start invading, and Japanese general Gotou (Chaos) wants to summon the old gods of Japan to get rid of the Americans and let the demons coexist with humans. Both of them ask you to kill the other and destroy their opposing faction, but there's nothing stopping you from wiping outboth sides.
Shin Megami Tensei: Strange Journey presents you with a dilemma in Grus. A demon has sealed the path to Maya, the area's boss, and demands that you kill the newly-pacified Jack's Squad before he'll let you through. However, the newly-angelic Zelenin offers you another option: use her song to brainwash the demons and make them open the path. Killing Jack's Squad is the Chaos option, while using Zelenin's song is the Law option. There is, however, an unpresented Neutral third option: Kill the demon that's sealing the path in the first place.
Spec Ops: The Line uses this as an actual game mechanic in places. The game will offer two (horrible) choices to the player, but will acknowledge other actions as answers without explicitly stating them. For example, the player comes upon a man accused of stealing water and a soldier who used unnecessary force against him, both of whom were sentenced to death and are hanging from nooses. The player is asked to choose which of them is guiltier. Snipers just ahead will shoot out the rope of the one the player doesn't condemn—or shoot at the player if he refuses to choose. In addition to the options of shooting either man or doing nothing, shooting at the snipers or shooting the ropes themselves are also considered valid responses.
In the final puzzle of Star Trek: A Final Unity, Picard is forced to choose between using a superweapon to annihilate a Borg Fleet, or simply using it to nonviolently halt their invasion. Naturally, the correct choice is None of the Above.
About all the solutions in Star Trek: Borg are almost never either the two choices given to you, but an absolutely insane third option that nobody would try on their first time. Thankfully Q gives you lots of tries...
In Star Wars: Knights of the Old Republic, there is a quest of sorts presented to you on Dantooine by a Twi'lek Jedi named Bolook, who is investigating a recent murder. The two suspects, Rickard Lusoff and Handon Guld, must be questioned in order to determine which one actually killed the victim, a farmer named Calder, in addition to corroborating evidence with an information droid. After 4 rounds of questioning, and calling both parties on false testimony and possible motives, you find that they were both guilty, and that Calder was sleeping with Handon's wife and had a business deal with Rickard which went sour. This gets you the more than double the XP of just naming one murderer.Full Details
In the fifth chapter of Strong Bad's Cool Game for Attractive People, Strong Bad needs some tech support. Unfortunately, the guy on the phone isn't interested in helping and tries to impersonate a voicemail system with multiple responses if Strong Bad says "One," "Two," or "Three." None of the responses are helpful to the player; the way to proceed is for Strong Bad to take a fourth option and say, "Four." This causes the tech support guy to panic and concede defeat.
The entire plot of Tales of Symphonia revolves around the protagonists' efforts to Save Both Worlds despite their condition of being in a hourglass-like state where life-giving mana must flourish in one and decline in the other - there isn't enough for both. And the whole process starts with the hero refusing to sacrifice The Chosen One in order to save his own world, insisting that he'll find a way to save both of them and the other world as well. He does, but it's sure not easy.
In "The Fall of the Samurai" DLC for Total War: Shogun II, you pick one of the three clans allied to the Emperor or one of the three clans allied to the Shogun. You can switch allegiances at any time. Close to the end, after you've conquered many provinces, you are given a third option: screw both the Emperor and the Shogun and try to go after the total control of Japan yourself (well, technically, your stated goal is to create a republic, but that has zero effect on the gameplay). This doesn't immediately ally everyone against you, and the Boshin War continues as before, with the only difference being that there is now a third power seeking to take charge.
Twisted Metal: Head-On has one of these in Agent Shepard's ending. The winner of the Twisted Metal Car Fu tournament gets a wish from Literal GenieBig Bad Calypso; typically they get screwed over. Rather than fall for this, Shep decides to just arrest Calypso.
Tyranny actually offers two third options. The obvious options are to side with the Disfavored or the Scarlet Chorus... but, less obviously, the player can also choose to side with the Rebels or to take a fourth option... and kill all of them. It's pretty unclear, even at the end, which is the morally 'right' side.
The Walking Dead Season Four has one of these in the final episode, but it's unique in that someone else makes this decision for you. Clementine, while escaping a group of walkers with AJ, is bitten on her leg, which is already heavily lacerated. She immediately accepts her fate, but AJ is devastated at the idea of either executing the girl who's taken care of him and been with him since birth, or watching her turn into a walker. The two of them make it to a barn, with Clem looking like she's on death's door, and after she prepares AJ to go find his way back to their friends and goes over with him of the fundamentals of surviving, she gives him instructions to other kill her or leave her, and he tearfully brings her axe up over his head; cue a Smash to Black, and you're suddenly playing within a flashback sequence, all while thinking that Clem has died. But once the game returns to present day, you find out that no matter what you told him to do, AJ decided to disobey and instead take the axe to the lower half of her leg, lopping off everything below the knee, and stopping the infection. She's grateful that he chose to do what he thought was right and "make the hard call."
In Wing Commander III, at one point you're given a choice between kissing Rachel or Flint, which would make the one not chosen mad at you (and thus unavailable, leaving you to either fly short a wingman or configure your own ship loadout if you don't want to launch without missiles, respectively). However, you can choose to not kiss either of them, by bypassing the decision scene entirely, and have both still available. Both will be unhappy with you and their morale will take a small ding, but only for Flint does that really matter, as lowered morale makes her flying less effective.
World of Warcraft has a neutral race, the Pandaren. At the end of their starting zone, players are given a choice to join the Horde or the Alliance. One player, Doubleagent, famously chose to pick neither and instead slowly ground his way up to the max level by farming herbs and other resource nodes over the span of two years, becoming the game's only top level neutral player.
In Yu-Gi-Oh! Nightmare Troubadour, when Marik possesses Joey and draws you into a Shadow Game, winning the duel will cause Joey to die, while losing means you will die. The only way to win is to force a draw using Ring of Destruction and Self-Destruct Button, which Yami Yugi is kind enough to give you before the fight begins.
Used in Zork Zero. You're faced with being executed, along with several other people, and everyone gets to make a last request. If the executioner can do it, he hangs you. If he can't do it, he beheads you. When it's your turn, the correct request is "executioner, cut my head off." So he'd have to cut your head off, then hang you. But he's only supposed to cut your head off if he can't do it, and you wouldn't have a head or neck anymore to be hanged from... The executioner eventually gets upset and has you tossed out. If you go back in, the executioner has come up with a third execution method just for wiseacres like you.