* When everyone joins Milo to stand with the Atlanteans against [[spoiler:Rourke. Audrey kicks the car door open, marches over to Milo, drags 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]].
* 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.
* The letter to Mr. Whitmore at the end, with the present from Milo along with a picture of Milo and his grandfather.
* Kida [[spoiler:becoming [[TheHighQueen a Queen.]] And we see her wearing a dress for the first time...]]
* 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.
* 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.]]
* 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.]]
* 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.