- The ending of "Where No Man Has Gone Before", while the ship and crew survive intact (for the most part) it still feels like a downer ending. The fact that Kirk points out that they couldn't save Mitchell somehow makes it worse. He was essentially Kirk's brother (making his absence from the 2009 movie both annoying and painful) with both men forced to turn on each other; Kirk to protect his beloved ship and crew and Mitchell intoxicated and corrupted by godlike power that he never asked for; especially evident during his few brief moments of lucidity near the end of the episode, where both times, all the poor man can say is his best friend's name.
Kirk: He didn't ask for happened to him.
- Spock's reaction to the Psi 2000 virus in "The Naked Time." The incurably stoic Vulcan breaks down in sobs. His explanation to Kirk of his regrets might also count, especially since Kirk is too pressed for time to listen.
Spock: Jim...when I feel friendship for you, I'm ashamed.
- Spock says about Omicron Ceti III that for the first time in his life, he was happy. Awww, Spock!
- The death of the Landru machine in "The Return of the Archons" was surprisingly sad in its own way. While Kirk was right in destroying it, hearing Landru cry out for its creator to save it as it exploded makes one wonder if perhaps the alien computer was sentient after all.
- The Downer Ending of "The City On The Edge Of Forever"
McCoy: I could have saved her! Do you know what you just did?
Spock: He knows, Doctor... he knows.
- What makes it even more effective is that as Spock says this, the camera pans to Kirk, who is completely breaking down in tears. He does not come anywhere close to tears again until Spock's death in Star Trek II: The Wrath of Khan.
- Kirk's solemn last words of the episode just put the cap on it. He sounds gutted:
Kirk: ...let's get the hell out of here.
- The original screenplay by Harlan Ellison was even more of a tearjerker, especially thanks to the inclusion of a legless World War I veteran called Trooper who is murdered as a result of the Enterprise crew members' presence in the past. Unlike Edith Keeler's survival, Trooper's death doesn't affect the time stream, and Kirk's reaction to the idea that the poor guy's life didn't matter is wrenching.
- "Amok Time," after Spock thinks he's killed Kirk.
T'Pau: Live long and prosper, Spock.
Spock: I shall do neither. I have killed my captain... and my friend.
- This exchange is even more tearjerking when you consider the Fridge Horror factor of Spock's first sentence. He fully expected either to commit suicide or to essentially waste away from griefnote (it's not certain which).
- Spock's horrified expression when he comes out of the blood fever and realizes what happened. You can easily imagine the poor guy's thoughts as he shuts down.
- Spock's background potentially makes this even more heartbreaking. The guy has already gone through an amount of discrimination and bullying note that has driven some people to villainy or to suicide, and his only response is to close himself off and work harder for acceptance. But when he realizes he's killed one of the only people to accept him (even if it's not really his fault), he breaks instantly, shutting down and wanting to die.
- Leonard Nimoy loved this episode and threw himself into it, doing some of his greatest acting ever. He later said that in the "I shall do neither" scene he was holding back tears and could barely speak the lines. Although he denies he or Shat did anything deliberate to suggest the HoYay some fangirls insist is canon, he says that the "I shall do neither" line best defines Spock's attitude to Kirk.
- It's a small moment, but in "The Apple" when Kirk finally catches the strange figure following the crew around the Everything Trying to Kill You forest, he grabs him and punches that sorry bastard right in the face. And the poor guy is horrified, and starts crying, because as it turns out, violence just isn't a thing on this planet. An apologetic Kirk immediately has to reassure him that they come in peace.
- "The Doomsday Machine". Decker's anguished description of how he lost his entire crew.
Kirk: Matt, where's your crew?
Decker: On the third planet...
Kirk: There is no third planet!
Decker: (looks up at Kirk in horror and shame) Don't you think I know that? There was, but not anymore! They called me, they begged me for help — four hundred of them! I couldn't... I-I couldn't...
- Also, Kirk begging Decker to come back and let them find another way besides a Heroic Sacrifice to destroy the creature. He doesn't listen.
- From "Journey to Babel", the scene between Amanda and Spock: recounting his painful childhood, her storming out in tears, his raised hand at the door, unable to do anything more...
- Captain Kirk's descent into senility and paranoia in "The Deadly Years" is made more painful by the reactions of those around him, and especially Spock, who looks sadder and sadder as the episode progresses. When after the competency hearing Kirk calls him a traitor and adds he never wants to see him again, Spock leaves looking (by Vulcan standards) like he's about to cry.
- "All Our Yesterdays". Kirk is able to get Spock and McCoy back to the present, but Zarabeth, the woman who helped them, the woman Spock has come to love, has to remain behind, condemned to live out the rest of her life alone in Sarpeidon's ice age past.
Spock: It happened, but that was five thousand years ago and she is dead now. Dead and buried long ago.
- The ending of "The Paradise Syndrome". Kirk loses his unborn child and his wife within minutes of one another.
- The deaths of so many Red Shirts. Yes, the death of Red Shirts was a Running Gag. But let's be honest, some of these deaths were very heartbreaking.
- Poor Yeoman Thompson, the only female redshirt to die onscreen in TOS, who was turned into a mineral cube by Rojan and crushed in "By Any Other Name".
- The young engineer Harper, who got vaporized by plasma flow activated by computer M-5 to restore its power supply. The worst part is how Daystrom tried to rationalize it as Harper simply "getting in the way."
- While it's not mentioned afterward (figures) the two security officers who got beamed into open space while Sulu and Chekov were under the induced illusion that the ship was still in orbit of a planet in "And the Children Shall Lead". Poor guys...
- The death of the man who was about to be married in "Balance of Terror," and his fiance's reaction at the end of the episode, is probably the saddest one in the series.
- Part of this is that, Running Gag it may have become, to Kirk, the fact that these crewmen died on his watch is clearly a personal failing - he may have saved the ship, but his role as captain is to protect those men and women under his command, so to him, not coming home with everyone means he still failed.
- Maybe "And The Children Shall Lead" isn't the greatest episode, but it does have a couple of tragic moments, most notably the happy smiles from the children looking at footage of their parents, which turn to horror and tears when they discover their parents are all dead.
- The Downer Ending to "Let That be Your Last Battlefield" where Lokai and Bele lose their home planet, their entire species' and even then still hate each other... because that hatred is all they have left.
Sulu: But the cause they fought about no longer exists. Does it matter now which one was right?
Spock: All that matters to them is their hate.
Uhura: Do you suppose that's all they ever had, sir?
Kirk: No, but that's all they have left. [dejected] Warp factor 4, Mr. Sulu. Starbase...4.
- The ending of "Charlie X" is nothing but pure horror and heartbreak.
- "The Immunity Syndrome": after Spock is chosen over Bones for the dangerous mission, Bones walks him down to the hanger deck, and Spock tells him, with just a touch of sarcasm, "Wish me luck." Bones refuses to say it until Spock is out of earshot. Later, when Spock's mission seems to have turned into a suicide run, Spock calls over the comm, "Tell Dr. Mc Coy he should have wished me luck." The look on Bones's face...
- While he certainly wasn't very likeable, Apollo's death at the end of "Who Mourns for Adonis" was surprisingly sad, with his final moments making him out to be less a ruthless tyrant than a Jerkass Woobie, who just wanted to be loved. In the end it's easy to empathize with Kirk and McCoy when they lament being forced to fight him.
McCoy: I wish we hadn't had to do this.
Kirk: So do I. [The Greeks] gave us so much. The Greek civilization, much of our culture and philosophy, came from a worship of those beings. The way they began the golden age. Would it have hurt us, I wonder, just to have gathered a few laurel leaves?
- The Bittersweet Ending to "Requiem For Methuselah." Kirk loses a woman he fell hard for - even though she was an android - and Kirk ends the episode face down at his desk in sadness. Which leads to this conversation between McCoy and Spock, which ends in a very poignant moment:
McCoy: You see, I feel sorrier for you than I do for him. because you'll never know the things that love can drive a man to - the ecstasies, the miseries, the broken rules, the desperate chances, the glorious failures and the glorious victories. All of these things you'll never know, simply because the word "love" isn't written into your book. Good night, Spock.
[McCoy leaves, and Spock quietly walks over to a sleeping Kirk and gently applies a mind-meld]