The 100 Season 2 is built around taking Clarke, originally an Actual Pacifist and All-Loving Hero, and putting her in situations where she has to Shoot the Dog. These include executing her Love Interest to secure an alliance with the Grounders, allowing hundreds of her allies to die to avoid blowing a double agent's cover, and ultimately committing full-on genocide against Mount Weather, all in the name of protecting her people. By the season finale, she's shot the dog so much that she can no longer see herself as a good person, and instead views herself as someone who commits evil so that others don't have to.
24: Jack Bauer has been called upon to do this sort of thing numerous times during the series run, often to create plausible deniability for higher-ups during times when he's not officially on CTU's payroll. Examples include executing and beheading a witness in a criminal prosecution (to get undercover with the man he was to rat out); staging the execution of a captured terrorist's children (to get him to talk); breaking the ringleader of a drug cartel out of a maximum security prison (to intercept a bio-weapon his cartel was about to buy); threatening to expose a terrorist's innocent daughter to a fatal virus (to make him talk); threatening to kill a suspect whose lawyer had exempted him from questioning (again, to make him talk); invading the Chinese consulate and kidnapping a Chinese national, and sacrificing his lover's estranged husband (who took a bullet for Jack early in the day) to save said national, ultimately ending up in a Chinese prison for it (to insulate the US government from reprisal); and hijacking Marine One and holding the President hostage (to get a confession of the crimes he'd committed). He also does shoot a dog, but that was in self defence. His shooting dead of Nina Myers in Season 3, on the other hand, was plain revenge-fuelled murder.
Angel: The crew, consistently and awesomely due to this show being Darker and Edgier than its parent show. For example, Wesley torturing a female druggie, Angel allowing Darla and Drusilla to kill a lot of Wolfram & Hart employees, and anything the recurring villain Holtz ever does.
Babylon 5: This show is full of this. Then again, every race and every individual in Babspace is a Magnificent Bastard — even the heroes are like this at times.
Even one of the most sympathetic and innocent characters in the series, Vir Cotto, has done this. He was the one who actually killed Emperor Cartagia. A necessary action, if extreme, and no one (least of all him) wished that it had to be done.
Bangkok Hilton: In the backstory, Hal Stanton thwarted a plan by Allied soldiers to escape from a Japanese POW camp in Thailand, as he knew that their captors would execute two prisoners for every one that escaped, a factor that the escapees refused to take into account. As a result, eight escapees were executed. The worst part? The guards themselves escaped the very next day when it turned out that the war was effectively over.
Has made this an almost weekly theme. Laura Roslin and Saul Tigh are the show's unquestioned champions - the former going so far as to kidnap and fake the death of a newborn unbeknownst to her parents and the latter going so far as to poison his own wife in order to give her a peaceful death after she was caught collaborating with the Cylons. (Probably the kindest thing he could have done, seeing what happens to other collaborators in the very next episode.) Reports of her death might have been exaggerated.
Al-Queda-style suicide bombing and planned genocide via biological weapon!
Canine execution via firearms starts up in the pilot miniseries and just keeps on going. Leaving behind ships that can't jump to FTL and Helo gunning down a man trying to jump onto an already-full Raptor are just two of the ugly decisions characters make. And things get worse as the series progresses.
Bones: Played with in the episode "The Man in the Cell". Bad guy Epps goes over the balcony rail, Booth lunges and catches his wrist, there's a long moment (and some really creepy dialogue from Epps)...and then Epps is street pizza. Did Booth let go or not? This turns into a sub-arc over the next few episodes.
Giles prevents the hellgoddess Glory from ever returning by suffocatingher human vessel Ben. He specifies that he's doing this because...or so that...Buffy never would. (The page quote comes from earlier in that episode, where he foresees having to do such a thing with Dawn.)
This does create some Moral Dissonance because only two episodes previously, Buffy's fight with the Knights of Byzantium explicitly resulted in nearly a dozen deaths, including one knight killed when Buffy threw an axe into his chest. This, however, happened in battle with well-armed and armored warriors, not to a currently-helpless, badly-injured person.
In a later season, the show having gotten a bit darker or at least grayer, Giles confronts Buffy about whether she would make the same choice again (Dawn vs. Saving the World) and she admits that life has taught her some dogs have to be shot and now she would sacrifice even Dawn if she had to in order to prevent the Apocalypse. She even outright tells Principal Wood she would be willing to let Spike kill him if Wood forces the issue, because Spike is the more useful soldier in the coming battle and she has to make the tough decisions if the world is going to survive.
Buffy herself has had to shoot the dog. In "Becoming, Part II", seconds after her vampire boyfriend Angel has his soul restored, the ritual he performed when he was the soulless Angelus kicks off and threatens to drag all of Earth into Hell. The only way Buffy can save the world is by killing Angel and consigning him to Hell instead...which she does.
Wesley tries to get the group to do this when the Big Bad of Season 3 tries to bargain with them using Willow as a hostage. Wesley argues that the potential death of tens of thousands if they accept the deal far outweighs the certain death of one person if they refuse. Willow's boyfriend Oz breaks the Applied Phlebotinum that would be used to destroy the Box of Gavrok. The Scoobies give the Big Bad the box in exchange for Willow, deciding to simply ignore Wesley from that point on. It's in stark contrast to the Angel spin-off where Wesley's sort of advice tends to be the decision that's often much more likely to be taken.
Heck this was started as far back as the second episode after Jesse, Willow and Xander's longtime friend, winds up turned into a vampire. Before the final confrontation with Luke, Giles makes it clear to the two that while he may look like their friend, it's really nothing more then a monster and that they will have to kill him. When all said and done, Jesse winds up dispatched purely by accident.
In Season 9, this is Whistler regarding his actions in season 8. His plan was to create a better world where good and evil were balanced even if it meant sacrificing billions of people's lives.
In the season 2 finale, Michael has to kill Victor. It's partly a Mercy Kill, since Victor says that the people who're after them will take him apart if they get him, but it's mostly just an expedient move for Michael in order to get closer to the people who burned him. Considering Victor was trying to kill Michael up until about halfway through this episode, it's a Tear Jerker. Especially since the good guys have gone out of their way to avoid directly killing anyone after ten minutes into the first episode.
And in the season 3 episode "The Long Way Back", Michael shoots his "partner" Strickler, upon finding out that he had arranged for Fiona to be kidnapped and handed over to any one of the various people who wanted her dead, simply because she was a potential red flag in Michael's file. Strickler had already pulled a gun on him at that point, and was not particularly inclined to let Michael do anything to prevent the plan from going through.
The season 1 finale saw the sisters getting attacked by a demon who had a master of time on his side so that whenever the demon himself was killed by the sisters, the day would rewind and start over. The sisters discovered that the only way to stop this was to allow the day to end without vanquishing the demon. Prue cast a spell to fast forward the rest of the day but it meant letting Andy die as he had sacrificed himself to save the sisters in the third version of the day (Phoebe and Piper had died in the previous two versions instead).
The episode "A Witch In Time" had Phoebe getting a premonition of her boyfriend dying in a robbery and she saved him, only for the Angel of Death to keep trying to kill him that resulted in her and Paige being killed by demons. Piper went back in time and was forced to give Phoebe the wrong directions during the robbery so that her boyfriend would be killed this time.
Phoebe's rebellious high school self eventually took over her and she busted an old school friend out of prison and he went on a rampage, using her powers to his advantage. Once the cops were after him again, he ordered her to change his appearance magically. She and Paige made him look like Chris who was being hunted by demons. The demons then appeared and killed the man, thinking him to be Chris.
Played for laughs in one episode. Morgan has to go undercover as a crime boss. To sell his story, when he enters a meeting, he is on a cellphone (pretending to ) convince/order his lackey to shoot a dog. The other crime bosses there look either confused or disgusted.
The Doctor has often found himself taking this role; it's especially become a character trait in his ninth and tenth incarnations. Instances include, in "Dalek" sealing his companion in a bunker with a Dalek in order to prevent the Dalek from escaping, and drowning the children of a Giant SpiderEmpress in "The Runaway Bride" rather than letting them devour the Earth.
However, the Ninth Doctor gloriously subverts this trope in "The Parting of the Ways". Poised with a weapon capable of destroying the Dalek Emperor's fleet - along with all of Earth - he cannot pull the trigger. It's all the more satisfying (though heartbreaking) given his actions in "Dalek".
Arguably the worst example shown so far is in "The Fire of Pompeii", causing the eruption of Mt. Vesuvius, and the destruction of Pompeii, in order to save the rest of humanity from being turned into Pyroviles.
He also destroyed his entire species in order to end the Time War? Sure, the Time Lord authorities had gone Omnicidal Maniac by that point, but he killed everyone on Gallifrey, which presumably included innocents.
In the Doctor Who New Adventures novels set during his seventh incarnation, he would commit such morally questionable acts so often that he quickly turned into a Knight Templar, and remained so for most of the series.
In Eleventh Doctor episode "The Girl Who Waited", the Doctor tricks an older version of Amy into believing she can escape after thirty six years imprisonment, so she'll help him save the younger Amy from being imprisoned and thus becoming her in the first place. He's lying - the paradox cannot be maintained and one Amy must die. When she attempts a Meadow Run towards him, he slams the TARDIS doors closed, leaving her to die. And then he gives the gun for Rory to shoot with a Sadistic Choice: Rory must pick which Amy he wants to save.
The stand-out moment for the Fourth Doctor doing this has got to be him forcing Davros into ordering the destruction of the prototype Daleks by holding down his life support shutoff switch to torture him.
Has Crais offering to execute Aeryn's mother (who was sent to hunt them down and kill them) after they capture her so Aeryn doesn't have to witness it. He doesn't actually 'shoot the dog', he fakes it and offers a proposal to Aeryn's mom where she returns to the Peacekeepers and says the job is done in exchange for her life. Technically averted...
No, that's technically a Double Subversion. In a later episode, Crais DOES shoot Aeryn's mother to save Aeryn's life. Which is exactly the kinda material this trope is made of.
Mal is the rare lead character who never needs a side character to shoot the dog for him. He's more than willing to kill someone to protect his crew, and he does it on multiple occasions, even when killing them isn't strictly necessary.
In regards to the following three examples, it should probably be said that every single time Mal Shoots The Dog he is doing so because his patience level has reached Zero. Each time you can almost hear him say; "I don't have time for your Húshuō bādào.".
In the pilot, he shoots Dobson (a federal agent) in the face without hesitation because Dobson was threatening River.
In The Train Job, he kicks the King Mook into Serenity's engines — shredding the man into a mist of blood — because he threatened to hunt them down over a deal gone bad.
In The Message, he shoots Tracy for trying to take Kaylee hostage, when a simple explanation of the situation would have solved everything. But would Tracy have listened?
The culmination of Mal's "Shoot the Dog for the crew" mentality is shown in Ariel where he fully intends to spaceone of his own crew for trying to sell out two others to the Alliance for reward money.
Game of Thrones: Ned's killing of Sansa's direwolf Lady because, in his words: "The wolf is of the North. She deserves better than a butcher." It's worth noting that Ned refuses to ask or even let someone else take responsibility for Shooting The Dog, as shown with both Will the deserter and Lady. He even looks them in the eyes (and hears out their last words, in Will's case).
House: Had its doctors treat an Idi Amin-analogue called Dbala. Cameron says repeatedly that she hopes he dies, and makes moves toward convincing his second-in-command to seize power by killing him, but still treats him as best she can. Then her husband Chase instinctively calls out a warning that thwarts an assassin. Later, he hears the assassin's backstory (and some of the dictator's genocidal rant), and decides he can't live with having saved this monster's life, so he fakes a test result, deliberately causing the dictator's death, which eventually causes Cameron to leave him and Princeton Plainsboro Teaching Hospital.
The opening scene of the first episode of House of Cards shows congressman Frank Underwood putting an off-camera dog out of its misery after its been hit by a car by choking it to death. He does this while monologuing about doing what's necessary to end suffering.
Eko shoots a man to keep his little brother from having to do so.
Later, a flashback shows Sayid killing a chicken on his father's order after his older brother refuses to do so.
The time Sayid shot 12-year-old Ben Linus to try and avert all kinds of bad stuff in the future.
Merlin1998: In this series, Merlin helps Uther rape Igraine by deceit, reasoning that it will stop the war, save many lives, and result in Arthur's birth.
Merlin: In the new BBC series, Merlin is forced to poison Morgana, who he has been lying to about her magic and hiding his own from, because she is the vessel for a curse that has caused all of Camelot to fall into a sleep they cannot awaken from. Admittedly, his hand was forced by Kilgharrah the dragon and Morgause only made things worse, but up until that point, he had viewed Morgana as a great friend and there was even a little bit of romance between them. He also betrayed the location of a Druid camp that he'd led Morgana to in hopes that she would learn more about her magic because Uther was hunting down innocent people and killing them to find her. This also kickstarted Mordred's hatred of Merlin.
NCIS: Gibbs shooting through Agent Michelle Lee to take out the Weatherman. And she asked him to do it! Complete Tear Jerker, right there.
New Tricks: A literal example of this trope is demonstrated in the pilot's opening after Sandra Pullman shoots a dog in self-defense during a bust on an Asian cockfighting ring. This incident and the bad publicity that results leads to her being assigned to start the Unsolved Crimes and Open Cases Squad (UCOS), the premise of the series.
"You shoot one dog in this country!"
Pie in the Sky: There's one episode where WPC Cambridge arrests an old police friend of Crabbe who's guilty of taking a bribe, to spare Crabbe from having to do so.
Person of Interest: In Season 2 Episode 9, one of the bad guys says this literally about Bear, the dog mascot of Team Machine.
Christian agrees with Johnny Royalle's plan to kill Wolfe, while intending to regain his own powers from Wolfe before killing him.
After Conrad Moody destroys the evidence linking him to Retro Girl's murder, Christian throws him out of the window.
Calista kills her abusive father after he robs a bank and asks her to help him escape.
Deena kills Morrison with her newfound powers in retaliation for trying to kill her partner.
Rome. The conspirators in the assassination of Julius Caesar try to kill Marc Antony as well, despite Brutus having forbid it. When Brutus call them out on this, they point out his Honor Before Reason. As he doesn't know of their actions, his honor is not besmirched. Brutus replies that actually he's twice dishonored, because now he looks like a fool for not knowing what his own followers were up to.
To put it bluntly, one must perform this trope to survive in the post-blackout world.
In episode 2, Rachel Matheson shot the Wiry Stranger to prevent him from stealing their food and because he put her little daughter Charlie in danger.
In episode 8, Tom Neville revealed to Monroe that Tom's friend Colonel John Faber's son was a rebel in order to prevent his son Jason from being executed and from being sent to California. In case you're wondering, Faber's son and his cohorts were shot on the spot off-screen, and the colonel is last seen being tortured on-screen because Monroe is not sure where the colonel's loyalties lie. Tom Neville had to have known that this would happen.
In episode 14, Miles Matheson wants Charlie to kill some Georgian soldiers to get their uniforms. Subverted Trope, because Alec Penner had already killed those Georgian soldiers.
In episode 16, Rachel shot Curt Thompson because he was going to shoot her and Aaron for stealing his food.
In episode 17, Rachel knocks out Lee Blackmore and leaves Blackmore's son to die. Deconstructed Trope, because she reveals to Aaron that she's not doing any of this for the greater good, but because she wants revenge against Monroe for Danny's death. In other words, she's doing it not because it's necessary, but because it's easier.
In the first season finale, Rachel wanted to abandon the wounded Nora Clayton in order to get the power back on, and Nora even urged them to just leave her. Charlie makes this a Defied Trope by pointing out that this is not an either-or situation. So, Rachel and Aaron go to get the power back on, while Charlie and Miles go to get Nora to the infirmary.
Sherlock killing Magnussen in the Series 3 finale, "His Last Vow", definitely qualifies, in a literal example (though more of a case of Shoot the Son of a Bitch). Sherlock blows Magnussen's brains out in front of John, Mycroft, and the police; since neither Sherlock nor John was under direct physical threat from Magnussen at the time, it's considered to be outright murder, and Sherlock is promptly exiled for it. However, Magnussen was an Asshole Victim who ruined countless lives with his blackmailing schemes, and was threatening to use his information about John's wife, Mary, to destroy both of their lives as well (and possibly even get them killed). Sherlock killed Magnussen in front of witnesses to protect them from this fate and to ensure that John was not blamed for the crime. And it's possible Sherlock wanted to make sure John was safe from Magnussen and was already pissed about the bonfire thing.
Lana Lang, Pete Ross, and Oliver Queen also used this ideology as justification for attacking Lex with lethal intent while under the influence of mind-altering substances. It seemed like this was the case for Kara Kent as well, but that was simply Brainiac in disguise.
Happens at least twice. Both times, it's a member of SG-1 killing someone dear to Daniel and explaining "I Did What I Had to Do". The first time, Teal'c killed Daniel's wife Sha're to prevent her Goa'uld from killing Daniel. The second time, O'Neill shot the android Reese to stop her replicator army, even though Daniel believes he had already managed to talk her down so the shooting was unnecessary.
In the first episode of Stargate Atlantis, Shepherd has to kill his CO after the latter has the life sucked out of him by a Wraith.
"In the Pale Moonlight": Garak and Sisko hatch a morally ambiguous plot to frame the Dominion for plotting an attack on the Romulan Empire, in order to get them to join in the war effort. This plot was recognized as a fake by a Romulan Senator who was promptly murdered by Garak. Though angry at first, Sisko eventually came to grudgingly accept that it was a necessity. While some fans consider this to be one of the best episodes in the entire series, others interpret Sisko's attitude at the end of the episode as Stupid Good; Garak did what Sisko's plan logically led to, but Sisko kept clinging to a vision of himself that was incompatible with what he actually wanted — Romulan intervention in the war to save Earth and the Federation. Then again, Garak explicitly calls him on this ("That's why you brought me in, remember?") and points out that the self-respect of one Star Fleet officer (plus a few not-so-innocent dogs getting shot) is well worth it as a cost for saving their entire region of the galaxy from the Dominion in the long-run.
Star Trek: The Original Series: In the second pilot "Where No Man Has Gone Before", Spock recommends that Gary Mitchell be killed before his growing power gets completely out of hand. Kirk initially rejects the suggestion in favor of merely marooning Mitchell, but finally realizes that he has no choice (and almost gets killed himself because he hesitates the first time he has an opportunity to go through with it).
Star Trek: Voyager: In "Prime Factors" Voyager's crew come across a race of aliens who have the technology to get them home, but who refuse to help them. A faction within their society agrees to covertly give them the technology in exchange for Voyager's library (stories being used as currency). However the transaction is illegal and Janeway refuses on principle. Some of the more militant crewmembers decide otherwise, only to be busted by Security Chief Tuvok, who then proceeds to make the exchange himself.
Janeway: I don't even know where to start. I want you to explain to me how you, of all people, could be involved in this.
Tuvok: It is quite simple, Captain. You have made it clear on many occasions that your highest goal for the crew is to get them home. But in this instance, your standards would not allow you to violate Sikaran law. Someone had to spare you the ethical dilemma. I was the logical choice, and so I chose to act.
More like "Shoot the Werewolf" in "Heart". Madison is a sweet, engaging Girl of the Week but also a danger to herself and everyone around her. She asks Sam (who's slightly in love) to do it as he's the only one she trusts, and she's unable to do it herself. Dean offers to do it but instead we hear a shot offscreen and end on Dean looking miserable and flinching.
This is Sam's character arc for season 4. Even with how badly it turned out, his intentions were good. This happens again in season 6 when Sam temporarily loses his soul and is willing to do anything (including letting his brother get turned into a vampire) to get the job done.
Finds a new dog to shoot in virtually every episode (as could be expected, given the consequences of failure and the presence of an emotionless android and a paranoid future soldier in the regular cast). For instance, in an early episode, the benign terminator Cameron prevents John from saving a suicidal girl, reasoning that he could draw attention to himself and risk getting exposed and drawing the attention of other terminators. The biggest example is Andy Good, an innocent computer engineer who will one day invent SkyNet, who gets shot (though Sarah's pretty upset about it).
In the episode "The Brothers of Nablus," Cameron guns down three thieves who stole from their house, simply because they knew where the Connors lived. Sarah spares the last robber, who was hiding in the bathroom. Cromartie eventually comes along and susses the location of the Connor's house from him.
Jack Harkness has taken up this role quite a few times, starting with giving a child to evil fairies to keep them from murdering innocents in "Small Worlds" and going up to sacrificing his own grandson in order to save millions of other children in Children of Earth.
A couple of more literal examples in killing Suzie and Lisa. Jack is very Needs of the Many guy.
The West Wing: Ends season 3 with Bartlet reluctantly ordering the assassination of terrorist leader and foreign diplomat Abdul Shareef. Bartlet sees this as an absolute wrong, but flawed evidence gathering prevents them from putting him on trial, and Leo convinces him that it's the only way to prevent future terrorist attacks.
The Wire: Done straight in Season Three where Cheese shoots his dog and the police mistake it as code and question him if he killed any of the murders that have been happening.
Ironic reversal: had Gabrielle saving her potentially-future-demonic-minion infant daughter Hope by not killing her in secret. Later events strongly indicate she probably should have.
Later events also give the impression that it might not have worked (she came back from being poisoned and the body burned, after all) and that Gabrielle might have been correct all along: Hope clearly cared for her mother and was hurt about being abandoned. Perhaps being brought up by a loving parent to teach her right from wrong might have done some good. Or perhaps not. Regardless, secretly not-killing her clearly didn't help.