When Booker is caught by the Vox Populi, he tries to get out of it by telling Daisy Fitzroy he has no quarrel with her or her followers, and just wants out of the city. Fitzroy is unimpressed, and strongarms him into helping her by making it clear that the Vox will kill him if he doesn't.
In the second part of the DLC Burial At Sea, Elizabeth is making her way through the newly war-torn Rapture when Ryan gets wind of her and contacts her wondering what she is doing in the city and offers to let her fight for him. She makes it clear she's on her own mission and doesn't want anything to do with Rapture or his war. But Ryan, paranoid as always of outsiders, takes that to mean she's a "parasite" and sics his splicers on her.
The AI in the Civilization series often act like this: Trade with them, or be considered enemy; trade with their enemies and also be considered enemies. This is particularly visible in IV; there, it's near impossible to stay neutral unless you have the forces and tech advanced so no one want to wage war against you anyway, unless you have a different religion as Isabella, who invokes "With Us or Against Us" on your state religion.
In Dead Rising 2, a group of redneck snipers aim to clean up America by eliminating those who don't agree with their ideology. This includes pansies, floozies, bureaucrats, liberals, and "them half-assed" conservatives. One of them says "if you ain't with us, you're against us".
Diablo III: Due to their half-angel half-demon heritage, humans of Sanctuary are utterly hated by most angels and demons, to the point of being obsessed with killing them even more than their "eternal enemies." The madmen among humans tend to return the sentiment. Examples include:
Demonkind decided to stop fighting angels and focused specifically on mankind, recognizing their potential and their corruption of evil itself. Belial and Azmodan in particular wage bloody and costly war instead of taking the smart route and stealing what they need to destroy everyone - their hatred of humanity is that immense. It is no wonder it eventually bites them in the ass, as the player character manages to figure out the Lord of Lies and utterly decimates the armies of the greatest military commander of the Burning Hells.
Angelkind could not stomach the demonic corruption of humanity, and left them to die as they focused on defending the High Heavens and fighting in pandemonium, even as the armies of the damned were routed straight to Sanctuary. Imperius constantly berates the player character, and Malthael went insane with a thirst for human souls.
Some humans find both of these attitudes disgusting and plan to kill anyone in their way, regardless of alignment. Examples include Zoltun Kulle and the Templar Grand Master.
Unfortunately, this attitude is starting to bite the ass of all sides when the Humans managed to produce a God-like champion called the Nephalem, who has the power to wage a one man war against heaven and hell alike and is violently protective of humanity.
Dragon Age: Origins: The Big Bad Loghain's game-long paranoia regarding Orlais (Fantasy Medieval France), and his conviction that they're using the the Blight as a smokescreen to send in Grey Warden spies to infiltrate and retake Ferelden (Fantasy Medieval England) from within, becomes so intense by the end-game that he's convinced that you're either with him and thus the nation's continued freedom, or you're against Ferelden's independence and are an Orlesian spy/sympathizer.
In Dragon Age II, tensions between the mages and the templars in Kirkwall reach a peak when Anders blows up the Chantry that Hawke is forced to either side with the mages and protect them from the Templars or side with the Templars and exterminate the mages.
By Act III, Meredith is so paranoid that she believes that anyone who disagrees with her is a blood mage's slave. She refuses to acknowledge the possibility that her fellow Templars might disagree with her entirely of their own free will. You're either with her, or with the blood mages. This gets even more pronounced when she whips out her lyrium idol sword, which was the cause of Bartrand's insanity and also what pushes her to the edge.
By the end of the game, Anders has deteriorated to the point that anybody who does not explicitly share his exact opinions on mage freedom fighting is just as bad as an enemy. It's difficult to say how much of this is from Anders himself and how much comes from Vengeance.
Dragon Age: Inquisition: Sera claims to dislikes elven culture's "us against them" attitude toward humans, yet ironically holds this view between nobles and commoners, and "elfy elves" verses everyone else. It also comes to a head in her romance with a Elven Inquisitor, as she'll force you to choose between your elfy beliefs or the relationship.
In Morrowind, Balmora Mages Guild Stewardess Ranis Athrys has this attitude toward any mages who are not members of the Mages Guild, and many of her quests involve sending you after these outsider mages. While convincing them to join is her preferred outcome, she will also accept killing them as a valid solution to the problem. Either way results in one less mage who is not a member of the Guild.
Ulfric Stormcloak is like this. In the words of Jarl Balgruuf:
Balgruuf (paraphrased): "To not fight with him is to side against him!"
Jarl Balgruuf of Whiterun is desperate to try remain neutral in the conflict. When first asked what side he supports, he replies "Whiterun's." He eventually is forced to choose, however (as pointed above, Ulfric does not take kindly to that kind of answer) and lends his support to the Empire.
After a certain point in the main quest the Blades discover that the Dragonborn has been working with Paarthurnax, who is a dragon and the former right hand of Alduin, and they refuse to cooperate with him any further unless he kills Paarthurnax for his past crimes against mankind. The player doesn't have to do this to finish the main quest, but the Blades cannot be convinced to let their grudge go.
Delphine: "It's your choice Dragonborn: us or him."
In Fire Emblem Fates, both Hoshido and Nohr nations will treat you this way if you choose one side over the other, especially in the Revelations path if you choose neither side. A few individuals do eventually warm up to you.
Edelgard's belief in this in Fire Emblem: Three Houses is the reason they end up as The Heavy on every route besides their own. Some of their opponents sympathise with their intentions, but Edelgard feels the only way to change the world involves defeating anyone who isn't absolutely on their side.
The Legend of Heroes: Trails of Cold Steel II: Duke Cayenne believes that all Nobles should be part of the Noble faction by default, despite the fact that many members of the lesser nobility (including Rean and Laura's fathers) disapprove of the goals and conduct of the Four Great Houses that lead said faction. He isn't above issuing open threats to try to convince said lesser nobles to align themselves with the Great Houses over the Imperial Government either.
Namm, the angelic god of justice from the Nexus War series, is so absorbed with the necessity of his war with the Manipulative Bastard demon lord Tlacolotl that he considers anyone not as dedicated to the war as he is to be at least a potential enemy. Casualties of this so far include mortals who haven't become angels fast enough, characters who fight for free will instead of goodness, and anyone who tries to sit the war out. Namm's attitude is the main recruitment method for Tlacolotl, yet at the same time Tlacolotl really is enough of a threat to the universe that it's not clear whether Namm is actually wrong or not.
Good!Cole: You're either gonna help me, or I'm gonna stop you... here.
This is also why Spike fights Parappa. Parappa questions Spike's constant pursuit of monkeys, and asks him if he dislikes fun. Spike comes to the conclusion that Parappa must be working for Specter if he's defending the monkeys at all.
RuneScape: When the Zamorakian Civil War broke out, most of the bandit gangs in the Wilderness were largely unaligned. After the Dark Warriors refused to fight in the war, the demons had their leader Cyrus killed, forcing the rest of the gang to flee the Wilderness and fight their way through anything that tried to stop them. During Unwelcome Guests, the Dark Warriors hire themselves out as guards for Fort Forinthry, where they quickly make clear that they have no love for the Zamorakians despite their own criminal history.
Saints Row (2022): The Idols are an anarchist group who claim to fight for the little guy against the oppression of the system. Except they routinely steal from and victimize said "little guys" and even take enjoyment in doing so. When called on this, they simply state that anyone who is not a member of the Idols is a cog in the machine and therefore complicit in the system, thus they are fair game.
Victor Saltzpyre of the Vermintide series subverts the trope somewhat by playing it far more compassionately. He is an ardent believer that everyone is either with Chaos or against them.... but in his case, it means that he is willing to join forces with factions the Empire is usually on bad terms with, so long as the end goal harms their mutual enemy.
The Scarlet Crusade believes its holy purpose is to destroy the Scourge. However, they believe that anybody who has not joined the Crusade is likely a carrier of the plague and is thus their enemy as well. Only when preparing to face Kel'thuzad have they grudgingly worked alongside other groups.
Garrosh officially adopts this philosophy as of Tides of War, declaring that all members of the Horde, even those who aren't in a military occupation (including civilians and shopkeepers) must swear absolute loyalty to him and him alone, or be put to death.
In X3: Albion Prelude, the Terran Conflict has this in spades in the war zones. The two human factions, the high-tech Earth State ("Terrans"), and their Lost Colony, the Argon Federation, are locked in a Guilt-Free Extermination War. Even if you're a loved Guardian of Earth in the Solar system and celebrated Federation Marshall in Argon Prime, the Argon Federation navy will blow your ships up left and right in the conflict zone because the Terrans like you more. The same applies with the Terrans if your reputation is ever so slightly higher with the Argon. If you're neutral with both, they'll take turns blowing your crap up. However, outside of these war zones both sides will happily sell you battleships even if they just blew your stuff up two systems over.
