- Meta example: Jim Varney died before the film was completed, and most of the production crew testify that he signed on knowing he wouldn't live to see the film's release. This, combined with the film's lackluster performance at the box office make the dedication to him doubly sad (At least somewhat medigated considering the film's become Vindicated by History).
- In the commentary the directors start to choke up a little bit when they remember working with him and refer to him as "That dear man."
- Thankfully, they only needed a sound-alike (Steven Barr, a.k.a. Urdnot Wrex) to fill in for him for one line in the original movie.
- As of 2018, watching the film and hearing the voices of the dear departed James Garner, Leonard Nimoy, Jim Varney, Florence Stanley, John Mahoney and David Ogden Stiers, is pretty rough.
- The expressions on the faces of the people in the prologue as they realize they're trapped outside the protective bubble, with the tsunami seconds from breaking over them. You can see couples holding each other just before the sea consumes the city.
- For that matter, young Kida crying for her mother as she rises into the Crystal.
- Speaking of Kida, the scene where she recounts what happened in the prologue to Milo. At first, the way she explains it starts out normally, but as soon as she brings up the crystal (or "star", as she thought it was) and subsequent loss of her mother, her voice significantly softens, almost as if even after all these centuries, it's still hard for her to talk about.
- The museum directors' treatment of Milo, from rescheduling his proposal meeting so they'll have an excuse to cancel, to Mr. Harcourt giving a rather withering speech to him. Fridge Horror sets in when you realize that, had The Call not intervened, Milo would've ended up just as broken as his grandfather.
- The moment during when Whitmore calmly mourns his friend Thaddeus, saying that he was a great man, but the mockeries of the other scientists broke him. Especially jarring since, until now, he had been portrayed as an eccentric and energetic old man.Whitmore: "If I could bring back just one shred of proof, that'd be enough for me."
- After the exciting battle with the Leviathan, Sweet setting a single candle in a helmet to drift on the water in the underground chamber, as a memorial to the many lives lost. Then Rourke comments they started with two hundred crewmembers, and they're all gone by the end of the movie...
- Becomes even sadder when you consider this movie came out during the same year as the 9/11 attack.
- A small one during the journey to Atlantis. Even though Milo is still the Butt-Monkey at this point and it's Played for Laughs, there's one where Sweet helps members of the crew up a small ledge, one by one. Milo, being last in line, reaches out his hand when it's his turn, but Sweet already turns to leave. Milo humbly recoils his hand, recognizing that he's not "one of the gang".
- When Milo shows Kida the Shepherd's Journal, it's revealed that the Atlanteans (including Kida herself) can't read their own language. Her lost expression is what sells it, the desperate attempt to remember a part of her own culture.
- The commentary even mentions that this is comparable to forgetting your own child's name, and somebody else knowing them better than you.
- In the Crystal Chamber scene, after Kida fuses with the Crystal, Milo softly, sadly calls out to her. It's a small moment where Milo knows that's not the real Kida before him.Milo: Kida...
- At some point in the movie, Rourke stepping on Milo's picture of him and his grandfather. For a moment, Milo can only give his betrayer a hateful glare. But when Milo salvages the picture from the broken frame, his expression significantly softens with despair.
- It's not just the picture that saddens Milo. He's looking back on how he meant for the Atlantis Expedition to make his grandfather proud. But instead, he feels as though his grandfather would be ashamed, if he only knew its crew all along planned to plunder the lost city of its riches (even if it meant taking the source of Atlantis' life force).
- Just the sight of the Atlanteans' crystals losing their glow, as the main crystal is being taken away by Rourke.
- The king telling Milo how he caused the destruction of Atlantis and the loss of his wife, and imploring him to save the city and Kida as he dies.
- And since Leonard Nimoy died in 2015, this has become even sadder.
- When Kida is released from the crystal, she comes out holding the bracelet her mother took off her (Kida's) wrist when the crystal took her. Given the implications, it's no surprise that Kida broke down in Milo's arms right after.
- The ending crosses over into Bittersweet Ending when you realize that essentially, Kida and Milo are holding an Atlantean funeral for Kida's father.
- The commentary even describes it as just that.
- The way the crew treats Mole counts. Sure, he's a Cloudcuckoolander who acts a lot like an animal, but it's clear he's not all right in the head despite being a genius at geology. And the fact that Audrey says he was a feral child for some time, and that most of the crew know that doesn't help.
Tearjerker / Atlantis: The Lost Empire