Tear Jerker / Stargate Atlantis

• Near the end of the pilot, the fate of Colonel Sumner. The female Wraith at first uses her telepathic abilities to find out about Earth. She then begins to feed on Sumner. Sheppard arrives, but not in time to save him. Being forced to administer ad Mercy Kill instead, ending the poor man's suffering.
• The Season 1 finale when John leaves on a suicide mission. Elizabeth catches him and...lets him go.
  Elizabeth: "You can't!"
  John: "I have to - and you know it."
  Elizabeth: "John...(shakes head) ...Go."
  • Especially heartbreaking in that she could have ordered him to stay, but ordered his death for the good of Atlantis.
    • Also Fridge Brilliance: You initially think John is performing the Heroic Sacrifice, then you realize its actually Elizabeth as well. John is giving up his life, but she's giving up her closest friend and sole confidante of the last year. Its a culmination of what the pair would do to protect their people after a season of protecting the expedition, and its heartbreaking.
• Perna's death scene in "Poisoning the Well".
• The fate of Ellia, the Wraith raised by a human, in "Instinct". While Ronon refused to see her as anything but a Wraith, Sheppard, Beckett and even Teyla were able to see that Ellia's human father had managed to make Ellia something different from "regular" Wraith, open to the idea that she could be something other than a killer. However, Ellia's own self-loathing of her need to feed ultimately drove her to take an untested medical treatment in the hopes that it would make her human, but instead the retrovirus turned Ellia into the very thing she was afraid of, culminating in Ronon killing a feral Ellia to save Sheppard's life.
• Ronon's flashbacks in "Sateda". They get increasingly poignant as the episode drags on, starting with him begging his fiancée to leave with an evacuation group while he stays to defend their world (knowing that he will almost certainly be killed), continuing with him watching his comrades and friends die all around him, and ending with him standing in a hospital, paralyzed with guilt over his inability to save everybody on the ward...and then his fiancée is vaporized by an explosion right before his eyes.
• Elizabeth refusing to submit to Koyla's demands in "Common Ground" and then having to watch him torture Sheppard over and over again.
• The episode "Sunday", which ends with Rodney talking to Carson, one last time.
  McKay: You were the closest thing to a best friend that I ever had.
• Not quite on the same level, but a particularly heart-wrenching scenario occurred when Dr. Weir told her fiancé Simon not to wait for her. He didn't.
• At the end of "This Mortal Coil", Rodney admits to Radek that he is distracting himself with fighting the Replicator invasion because he can’t face losing Elizabeth and how much he was hurting after Carson died.
  Radek: I know what you’re trying to do.
  McKay: Yeah, what’s that?
  Radek: Lose yourself in your work to avoid thinking about Elizabeth.
  (Rodney looks up from his computer but doesn’t turn around.)
  Radek: You must realise it’s only a temporary distraction.
  McKay (his voice full of pain): That’s one of the perks of the job. Something terrible happens, you don’t have enough time to dwell on it ‘cause you’re too busy trying to stop the next terrible thing from happening. Seriously, if it wasn’t for the Replicators and their plan to wipe out every human in the galaxy, I’d be in pretty bad shape right now.'''
  (Radek looks at him sympathetically.)
  McKay: No, this is Carson all over again and I’m just not ready to deal. Not yet.
  Radek: You're not the only one who misses him, Rodney. Don't suppose you want to talk about it?
  McKay: Evenutally, but not now.
  ...
  McKay (heartfelt): Radek, (beat) thank you.
  Radek: You're welcome Rodney.
• "The Shrine". The whole episode will make you cry for so many different reasons. Especially when the team pressure Woolsey to let them try to save McKay, and Ronon says that he could never understand. Woolsey then tells them of father's Alzheimer's, where his father didn't recognise him for months, before a moment of clarity where he was his old self... and then he was gone again.
  • Jeannie having to leave the room so Rodney wouldn't see her cry.
  • McKay running down the hallway, screaming for John like a scared kid looking for his dad. Given the circumstances and Sheppards role in the team, thats pretty much exactly whats happening.
• Elizabeth's death in "Ghost in the Machine". Heartbreaking enough that she's gone for the last time but what clinches it is John standing alone in the gate room, clearly on the verge of tears.
  • That one moment in "Ghost in the Machine". The city's systems shut down, one computer monitor suddenly brightens, and the team realizes that someone or something is trying to communicate with them through the computer itself. Rodney types in "Who are you?" and the answer comes slowly: "Elizabeth Weir" The music that accompanies that single moment is so absolutely perfect, it's as though the strings are saying "what have we done to you".
  • At the end of the episode, before stepping through the stargate to her death Weir turns back to look at Sheppard, and the two briefly make eye contact before he has to look away. They both look so sad, but Sheppard looks particularly heart broken. After all the replicants have gone through, John spends a long time staring at the gate, looking close to tears.
  • The revelation that McKay blames himself for what happened to Elizabeth
• Finding out in "Enemy at the Gate" that George Hammond has passed away. Doubly so since it counts a case of The Character Died with Him.
• A lot of the Atlantis Expedition's victories have an undertone of tragedy, as they often cross a lot of moral boundaries to get there. Notable is their defeat of the Asurans, which is nothing short of genocide. The title of the episode, "Be All My Sins Remember'd", is a quote from Hamlet meaning "Remember the evil I've done before you give me praise".

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