- Milo looks at a picture of a young him with his grandfather and has a flashback of trying on Thaddeus's helmet, but it's too big for his head and makes a thump noise as it falls over his eyes.
- Even in the present, it still makes a thump noise when he puts it on.
- The fact that Milo keeps a small shrine for his grandfather's helmet, showing that even years after his passing, and even in his adulthood, he still holds his grandfather in the highest regard.
- It's very, very minor and put into a very mean-spirited statement, but after Milo chases down Mr. Harcourt after he's essentially refused his expedition and told him to stay in the boiler room, Milo is driven to threatening to resign. Harcourt then actually stops his car and gives Milo some genuine if harsh advice not to turn out like his grandfather, as it's implied that Thaddeus's insistence on the existence of Atlantis is what drove the other board members to marginalize him. Harcourt does turn out to be wrong, but he didn't have to give Milo that advice and even admits that Milo has a lot of potential.
- Thaddeus' and Preston's friendship. Even after the death of his friend, Whitmore does everything in his power to fulfill the promise he made to him.
- Sweet is one of the few crew members who's openly nice to Milo upon their first interaction.
- In hindsight, Roarke bothering to have a small memorial for the lost crew members is this (and a Tear Jerker). Despite that he turns out to be the Big Bad, he still pays his respects to the 200 men and women who died.
- Milo, after causing mishaps and generally being the Butt-Monkey of the group, finally being offered a seat with the rest of the group at dinner, and all of them talking about the reasons how they ended up in their respective professions. And afterwards, Milo telling Audrey how his grandfather took him in after his parents died.
- Milo shares a story about the time he found an arrowhead during a camping trip with Thaddeus. During the telling, Audrey smiles at the story, and Mole (as creepy as he is) fusses over how cute it is. Milo's eyes during the scene adds to the cuteness.
- The few scenes where Milo reminisces about Thaddeus (the quick flashback in the beginning and when he talks about him to Audrey) just shows how much of a loving grandfather the latter was.
- In hindsight, the scene where Kida sneaks into camp counts as this, despite that she was wearing a scary tribal mask at the time. She rummages through Milo's stuff when she finds the photo of him with his grandfather. And she caresses the image so reverently, as though she can already sense its sentimental value.
- When Kida first meets Milo, he's injured from a recent misadventure with some fireflies. Without any further prompting, Kida uses her crystal necklace to heal Milo's wound. It's a Pet the Dog moment that marks the beginning Milo's relationship with Kida, because she was kind to him, not just because she's an Atlantean.
- Milo and Kida admiring the view of Atlantis. Also counts as a Tear Jerker when Milo grows teary-eyed at the memory of his grandfather.
- When everyone joins Milo to stand with the Atlanteans against Rourke. Audrey kicks the car door open, marches over to Milo, helps him onto his feet, and then glares at Vinny as if to say, "Get your ass over here or by God I will make you." Vinny nods, walks over, and wraps an arm around Milo, and suddenly the others gain their resolve and go to stand with them.
- Though they don't have much interaction, the amount of respect that Milo and the king have for each other is touching, especially before he dies, he entrusts Milo with returning the crystal, saving Atlantis and saving Kida.
- Just after to this, Sweet's speech to Milo.Sweet: It's been my experience that when you hit bottom, there's nowhere to go but up.Milo: Who told you that?Sweet: A fellow by the name of Thaddeus Thatch.
- That Sweet is the first one of the team to turn on Rourke after he fatally injures the King. Even though he joined the expedition for the money like everyone else, he proves that being a good doctor and a good person is more important to him, and his speech to Milo indicates that he is more loyal to him and Thaddeus than he ever was to Rourke.Sweet: I followed you in, and I'll follow you out.
- At the end of the movie, Milo and Kida don't even say two words...they just look into each other's eyes and hug. It's so simple, yet so heartwarming.
- However, there is one thing Kida says before they hug: "Milo". She's responding to earlier when Milo called out to her unresponsive crystalized form.
- The collective farewells from the crew as they leave Atlantis.
- Especially Audrey's. She straight-up kisses Milo on the cheek, and even playfully tells him "Two for flinching."
- A subtle one but Audrey is shown with Milo's cat at the end. She's taking care of it for him since he's too busy being the prince consort to Kida.
- The letter to Mr. Whitmore at the end, with the present from Milo along with a picture of Milo and his grandfather.
- Kida becoming a Queen. And we see her wearing a dress for the first time...
- In a meta example, despite the film's polarizing reception, Cree Summer has said that Kida is her favorite role - and she considers her an official Disney Princess even if she isn't in the line.
- Cree also said she was amazed that the Disney animators were in the studio sketching her as she recorded her lines - having not been used to that in most of her voice-over work - and that is one of the reasons Kida is her favorite role.
Heartwarming / Atlantis: The Lost Empire