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* 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.
* 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.
--> '''Whitmore''': [[{{Tearjerker}} "If I could bring back just one shred of proof, that'd be enough for me."]]
* Sweet is one of the few crew members who's openly nice to Milo upon their first interaction.
* In hindsight, [[spoiler: Roarke bothering to have a small memorial for the lost crew members is this (and a TearJerker). Despite that he turns out to be the BigBad, he still [[EvenEvilHasStandards pays his respects to the 200 men and women who died.]]]]
* Milo, after causing mishaps and generally being the ButtMonkey 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.
* 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 [[{{Understatement}} misadventure]] with some [[MakesSenseInContext fireflies]]. Without any further prompting, Kida uses her crystal necklace to heal Milo's wound. It's a PetTheDog moment marks the beginning Milo's relationship with Kida, [[BecauseYouWereNiceToMe 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 TearJerker when Milo grows teary-eyed at the memory of his grandfather.
* When everyone joins Milo to stand with the Atlanteans against [[spoiler: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]].
* 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 named [[TheGhost Thaddeus Thatch]].
* 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.
* A subtle one but Audrey is shown with Milo's cat at the end. She's taking care of it for him since [[spoiler: 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.
** Just prior to the above, when Audrey tell Whitmore that Milo [[BlatantLies 'went down with the sub']], he sadly [[ExactWords hopes that he's in a better place]], whilst looking at a picture of Milo and Kida holding hands.
** According to the commentary, this was based off the letter at the end of "It's a Wonderful Life".
* Kida [[spoiler:becoming [[TheHighQueen a Queen.]] And we see her wearing a dress for the first time...]]

* At the end of ''Milo's Return'', [[spoiler: Queen Kida uses the Spear of Destiny to raise Atlantis to the surface, surprising some fishermen who are quickly amazed at the sight. The last few lines from Whitmore are especially good to hear despite the Team Atlantis series not being picked up and provide a nice finish for the adventures of Milo and Crew]].
-->'''Whitmore:''' [[NothingIsTheSameAnymore The world was never the same after that day]]. [[HappilyEverAfter It was much better.]]