This is a common theme in the series. The main characters (who are only 13-16, mind you) are forced to do some terrible things to prevent both humans and countless other alien species being enslaved by a Puppeteer Parasite species. This includes trapping another kid in a rat's body because he turned traitor, killing sentient beings so their bodies can't be used as hosts, manipulating an Actual Pacifist to go against their nature to kill...in the very last book they kill tens of thousands of unprotected Yeerks. When they're accused of war crimes, this is their justification.
In A Brother's Price, Cira says this a couple of times while rescuing Jerin from kidnappers, some of whom she kills. She would, of course, normally not have exposed a delicate young man to such cruelty. In the backstory, some princesses, after seeing a play about a civil war, at the end of which toddlers were executed, reason that their ancestors did what they had to do, as any survivors would have led to a You Killed My Mother situation. That said, when faced with a similar decision at the end, they ultimately choose to Take a Third Option to avoid either option.
In Poul Anderson's "The Burning Bridge", when a message from Earth is causing people to want to turn back, The Captain fakes a more imperious message to inspire them to go on — and when he's caught, makes it appear that the crewmember had gone crazy and has them put him into deep sleep.
In the fourth Codex Alera book, Captain's Fury, the First Lord Gaius Sextus has one of these moments when he deliberately triggers a volcano over the city of Kalare, wiping out everyone in the city: rebels, civilians, and slaves all alike. He's forced to do this because High Lord Kalarus was planning to wait until hundreds of thousands of people, refugees and Legion troops from both his army and the loyalist Alerans had entered the city before triggering the volcano to kill everyone. Thanks to Gaius, only the city was wiped out, instead of the region. It did destroy all of the smaller towns and steadholts in within the ring of mountains surrounding Kalus, but it was still far less than would have happened if Kalarus had had his way. The two Cursors who guided him there, who had no idea Gaius was planning this, refuse to accept his justifications and resign on the spot.
Daystar and Shadow: When Robin feels guilty for interrogating some priests, then killing them for knowing too much and burning the church down, Shadow reminds him that it was necessary.
Discourses on Livy talks about how necessity must sometimes trump what is good for the sake of preserving liberty.
Subverted in Night Watch (Discworld) when Vetinari suggests that a monument be erected to the watchmen who died in the Glorious Revolution of May 25th, engraved with the phrase "They Did the Job They Had to Do." Vimes angrily replies, "No! They did the job they didn't have to do, and they died doing it, and you can't give them anything."
Reinforced and played fearlessly straight in Carpe Jugulum where Mistress Weatherwax declares that there are no shades of moral grey, "only white that's got grubby". In her view, when a thing is right, it's right, even if it gets your hands dirty.
In Summer Knight, Aurora says that she must stop the interchange between the Summer and Winter Courts, and it's horrible but she didn't set the price.
In Changes this is what Harry does. He'll go all out to do anything for his goal to save his daughter's life, including taking the position of the Winter Knight, killing the old one in the process, getting all his friends at risk of death, even destabilizing the White Council and most of all, killing his lover to use the very dark magic his enemies sought to use on him right back at them.
Harry:I used the knife. I saved a child. I won a war. God forgive me.
The witch Senna Wales of Everworld, as mentioned above, occasionally says something to this effect to the other main characters in reference to her schemes, which often involve some poor sap being bewitched.
In The Foundation Trilogy, one of Salvor Hardin's mottoes is "Never let your morals prevent you from acting correctly".
Raj Whitehall's computer mentor, a Well-Intentioned Extremist if ever there was one, and his wife Suzette are always telling him this one in The General Series. To Raj's credit he never quite accepts it.
Go to Sleep (A Jeff the Killer Rewrite): Liu's final words are "W-why?" after Jeff stabs him. He says that he had to, so his family would no longer need to live in this cruel world. Of course, this reasoning is dubious since Jeff has just snapped to his insanity.
Jeff: I- I had to Liu. I promise you'll go to a better place now. You'll be asleep with Mommy and Daddy, and not have to live in this sick and terrible world. Please, go to sleep.
One of the main themes of God-Emperor of Dune. Leto II has the ability to see the future to a (not entirely) unprecedented extent, and has seen that humanity, as a species, will die somewhere down the line if civilization is not altered from its present course. This leads him to turn himself into a tyrannical God-Emperor who ruthlessly and callously manipulates and uses everyone around him, and also includes limiting technology and a eugenics program. This state of affairs lasts over 3,000 years, and throughout it all Leto II is shown to hate what he's doing, wishing that things could have gone another way... but his future sight has determined that only through this despotism can he prevent the death of humanity. Eventually, his plan reaches its Byronic conclusion. The chaotic fallout from Leto II's assassination and the end of his oppression eventually triggers the Scattering: a galaxy-scale diaspora that eventually causes the human race to diversify, which is what Leto's visions had shown to be the way to save humanity.
The Grace of Kings: Kuni Garu genuinely feels terrible about attacking the rival king Mata Zyndu right after declaring peace, but believes that Zyndu's Blood Knight nature makes another war inevitable, so he owes it to his people to end Zyndu's reign as efficiently as possible, personal honour be damned.
In Halo: First Strike, intel agent Haverson shoots a perfectly nice Engineer who had just voluntarily fixed the Chief's armor. When questioned on it, he states that he'd have rather not done it, but he couldn't risk the Engineer being captured by the Covenant and providing them with information on the armor. note In the same book, Cortana realizes Covenant slipspace drives and practices are deliberately limited, and circumvents those limits to jump inside atmosphere. A Covvie AI leaks this info to its masters before Cortana can stop it. In Halo 2 and ODST, Regret's devastating slipspace jump over New Mombasa was only possible because of Cortana. Later, when the Gettysburg-Ascendant Justice is forced to abandon the Eridanus Secundus rebels to the mercies of the Covenant, Chief asks Whitcomb if they did the right thing; Whitcomb replies that it probably isn't, but that they have a duty to the people of Earth, not "a pack of privateers and outlaws". That said, he still clearly regrets it and mentions that there'll be a place in Hell for him for this.
In Halo: Ghosts of Onyx, Halsey actually invokes this; she asks Kurt why he added a bunch of illegal and dangerous modifications to the Gamma Company Spartan-IIIs, with Kurt replying that he did it so that Gamma might have a chance of actually surviving their battles. Halsey then says that they're not so different, and goes on to explain why she summoned him and the other Spartans to her.
In Halo: Shadow of Intent, Shipmaster Rtas 'Vadum gave the orders to quarantine and sterilize Flood-infected High Charity in order to prevent the highly-virulent parasite from spreading, despite the fact that a lot of civilians were still stuck there. Prelate Tem'Bhetek seeks revenge on him for this, as his wife was one of the victims. When the two finally have a chance to talk; Rtas reveals to Tem that he only gave the order after all his efforts to rescue High Charity's remaining citizens had failed, and it's clear Rtas wishes he could have saved them all.
This is a running theme in Hammer's Slammers: in war, you can't keep your hands clean unless you want to lose. The Slammers are well aware of this. Some of the groups that hire them are shocked to find it out — the hard way.
Both Dumbledore and Snape from Harry Potter. Also implied when describing Crouch's decision to allow aurors to use the Unforgivable Curses during the first war with You-Know-Who. And Harry himself doesn't come away all squeaky clean in The Deathly Hallows either, throwing around Imperius-curses left and right, not to mention when he uses the Cruciatus Curse against the death eater Amycus Carrow.
In Hero, Goran uses this exact phrase when Thom asks him how he got himself and his little brother out of their war-torn homeland. What makes it chilling is that that's all he says; we never find out what he actually did.
Hurog: In Dragon Bones, this is the justification Ward gives for working together with the villain, which includes giving the villain the eponymous dragon bones. Oreg doesn't buy it. They Take a Third Option in the end.
Livia in I, Claudius ruthlessly manipulates and kills family members and anyone else close to them to ensure her son becomes emperor and Rome does not return to being a Republic, convinced this is the only way for the city to remain great.
I'm the Villainess, So I'm Taming the Final Boss: Keith Elgrid, Claude's servant, started illegal demon trafficking with a landlord to get permission to borrow the latter's lands for demon refugees of Claude's forest. He only did so because of the threat of eviction, and he only picked demons who consented to be smuggled.
In the Imperial Radch series, the empire of the Radch fervently believes in the interdependent values of "Justice, Propriety, and Benefit", and Lord Anaander Mianaai claims that all of her actions, however heinous, are intended to benefit the Radch. Breq counters that when every individual Radchaai citizen knows that they could be killed on her whim, Mianaai's not doing a very good job of being Just or Proper and has a pretty self-serving notion of Benefit.
In Death: Eve and Roarke have had to defend their actions more than once and they have even said this trope practically word for word to each other.
Industrial Society and Its Future: Kaczynski only briefly mentions his bombings, saying he did them for attention so people would become aware of how industrial society oppresses humanity and must be destroyed, or else we all may turn into complete slaves of our technology. Getting the manifesto published turns out to have been entirely Kaczynski's goal with them. He claims otherwise if it was published very few would have ever read his work.
The Lensman universe generally leaves this as an unspoken trope for the good guys, but it's out there in black and white at the end of Triplanetary. The sum total of the mayhem each side has wreaked on the other is tallied up once hostilities have ceased, with those responsible on both sides declaring the trope and openly admitting they wish they could take it back.
Zack invokes this trope quite a lot in The Mental State in order to justify the extreme methods he uses to survive in prison and improve the quality of the prisoners' living conditions.
Brent Weeks' The Night Angel Trilogy is full of these, usually from Logan. When newly made King Logan flips a table, breaks a leg off and brutally smashes in the arms and legs of his best friend Kylar, who is slowly dying a torturous death on 'the wheel'. He then gives an ultimatum to the Laeknaught,shattering his "good boy" image. He also says this verbatim to Count Drake after he bends knee in allegiance to Terah Graesin.
When George shoots Lennie in Of Mice and Men. After Lennie kills Curley's wife, George is forced to shoot him so the other men don't. He does it in a way so Lennie doesn't realise, which the other men would not have given the courtesy of doing.
Mr. Sellars in Otherland, the Mysterious Informant for the good guys, is very much The Chessmaster and shamelessly manipulates people in order to advance his schemes, the most disturbing of whom is an innocent six-year-old girl. In the end, his justifications ring hollow even to himself, especially once his dark secret is revealed and it turns out that his core motivation was entirely selfish.
In the first book of The Queen's Thief, the Queen of Attolia is presented as a vicious tyrant who hangs disloyal barons from the walls of her palace, tortures anyone disloyal, and ruthlessly destroys her foes. The second book shows Tough Leader Façade, revealing that she is so ruthless because anything less would lead to either a forced marriage or a civil war, in which her country would surely come under the heel of a greedy baron that would carelessly bleed it dry. By making herself untouchable and terrifying, and giving no quarter to any disloyalty, Attolia ensures that her people have a ruler who actually cares about the well-being of all their citizens, not just the rich and powerful ones.
In Red Harvest, "a man's got to do what a man's got to do" is favorite phrase of Noonan the chief of police. Ironically, he uses it any time he does something that would benefit him — such as manipulating a witness to convince her that her husband's killer was the man he had a grudge against. The Continental Op repeats the phrase before searching a dead lawyer's pockets for potential blackmail materials.
A Song of Ice and Fire has several characters who will give this reason for their actions, but none can compare to the sheer lengths that Bloodraven went to to exterminate House Blackfyre and their claim to the Targaryen throne. He broke every taboo in Westerosi society, up to and including murdering Aenys Blackfyre under a flag of truce and diplomacy, in the pursuit of his goals. The murder of Aenys was considered heinous enough that his favorite grand-nephew, King Aegon the Unlikely, the direct beneficiary of that action, exiled him to the Wall for it. But this may well be a case of The Extremist Was Right, because Aegon's reign is largely untroubled by the threat of another major uprising by the Blackfyres.
The rulers of Kegan in a book of Jedi Apprentice made their planet into a Stepford-Smiling mess, but feel justified in not just doing it, but preserving the status quo. Oddly, they do seem to have actually made correct predictions about the rise of The Empire. However, even though they were correct, it wouldn't have done them any good; even isolated, there was nothing to stop the Empire from coming after them.
In Battlefront: Twilight Company, the Rebel Alliance infiltrates Sullust and captures a facility on a volcanic mountaintop. In preparation for the Imperial counterattack, they place scouts and ambushers in spiderholes on the slopes and base of the mountain. However, when the enemy cavalry arrives and begins to overrun the forward lines, the Rebel commander is forced to mortar his own troops.
In This Immortal, this is what Conrad's excuse for having founded Radpol as Konstantin Karaghiosis and engaged in prolonged guerrilla warfare, reducing the number of uncontaminated areas on Earth even further, boils down to. When Hasan points out that none of what they did changed anything in the long run, Conrad counters that at least their actions prevented the situation from getting worse.
Trapped on Draconica: Taurok hates every single order Gothon gives him over the course of the story but follows them to keep his family safe.
Inverted in the Vorkosigan Saga novel Barrayar: newly-made Regent Aral Vorkosigan is faced with either upholding the rule of law or sparing the life of a boy who accidentally killed someone in a duel—a crime punishable by death. He eventually chooses the law, but feels miserable about it. Even knowing that he Did What He... you get the idea... doesn't comfort him much.
The Inquisition's, and also Hyperion's, excuse for slaughtering the civilians and guardsmen who took part in the campaign to retake Armageddon. They argue it's better for a few thousand potentially corrupt souls to die than risk having to potentially slaughter millions of innocents in the future because they let the thousands live.
Inquisitor Kysnaros' view of why he is prolonging the conflict with the Space Wolves: in his view, not bringing them to heel runs the risk of the Imperium sinking into a civil war on a par with the Horus Heresy.
Grand Master Joros advises Kysnaros to open fire on Logan Grimnar's fleet, in the hopes of either forcing Grimnar to capitulate or taking him as a hostage to force the Space Wolves into compliance. He even admits this when Grimnar confronts the Inquisition forces, stating his actions were for the greater good. It results in Grimnar burying a power axe in Joros' chest and the Space Wolveseffectively declaring war on the Inquisition.
Gaunt's Ghosts: Colonel-Commissar Gaunt's justification for leaving Tanith to burn at the beginning of series is that the planet could not have been saved no matter what he did. It is the act of not letting the Tanith soldiers stay behind and die for their planet that invokes this trope. He made them 'ghosts' because that is what he had to do as a loyal officer of the Imperium.
Soul Drinkers: In Chapter War, the Inquisitor Thaddeus lied to get aboard a Howling Griffons' ship. When they came to a head, and they try to imprison him, he kills one to escape. He once "would have never accepted the death of a good Imperial servant as a necessary evil. But he was much wiser now."
In Warrior Cats, Hollyleaf gives this as a reason for killing Ashfur in order to prevent him from spilling the secret of her and her siblings' parentage.
This is a major theme in the series with the three male main characters forced to act progressively more brutal as their responsibility grows and the situation worsens. Includes such gems as using friends like pawns, executing friends, torture by way of dismemberment, allowing bad guys to enslave hundreds of women in order to secure a temporary military alliance, creating an army of superpowered men who will eventually go insane, and purposely destroying your own humanity in order to be up for the job of saving the world.
Inverted in that Rand's inability to kill any woman, even when she's a villain, causes his mentor to die.
In the Indian novel The White Tiger, Balram believed that the only way he could become an entrepreneur and break out of the coop was to kill Ashok. Hell, when you look at how things work, he was probably right..
World War Z has the Redeker Plan, which is basically a strategy for using refugees as zombie bait while government forces regroup. Despite the horrific inhumanity of the plan, the world's governments get so desperate that they use it anyway... and the plan arguably saves humankind (or, at the very least, prevents said governments from collapsing and leaving the world in anarchy).
This is Cauldron's go-to justification for all the horrific things they've done over the years: by way of Omniscient Morality License, they claim that doing anything else would have led to the extinction of humanity.
Alexandria justifies abducting innocents from other worlds, most of whom were about to die, and then experimenting on them in order to better develop Cauldron's super serum with this.
Later, Khepri tells Contessa that, while she would have taken other actions given the choice, she does not regret what she's done.
