At the Duckburg harbor, Donald Duck is preparing for a job interview while his nephews Huey and Louie enthusiastically help him get ready, which ends up causing messy results. After he discovers that the babysitter is unable to make it, presumably due to the boys giving her a new address, and his last nephew Dewey had attempted to hijack their houseboat without him around, Donald reluctantly takes the boys to Duckburg's billionaire-adventurer Scrooge McDuck, much to the boys' excitement.
Meanwhile, a sulking Scrooge is attending a business meeting with his advisors listening to his company's current stock. Once the meeting adjourns, Scrooge has his chauffeur, Launchpad McQuack, drive him by his money bin before heading back to McDuck Manor. However, he runs into Donald and the boys at the entrance. After a moment of tension between Scrooge and Donald, Donald introduces the boys to Scrooge as their formerly estranged uncle. While the boys are amazed at the revelation, Donald instructs Scrooge to watch over them while he attends his job interview. Before leaving, Donald cryptically stipulates that he keeps the boys out of trouble.
Inside the mansion, the triplets immediately hound their uncle with questions about the fantastic tales the billionaire was known for. Aggravated by their questions, Scrooge has his maid Bentina Beakley escort the boys to another room and locks them in there. Unwilling to put up with Scrooge's distance, Dewey tries to break out of the room, but the three are suddenly captured by a girl named Webby, initially believing that the triplets were perpetrators. She introduces herself as she befriends the triplets, and explains that she was researching Clan McDuck as Scrooge along with Donald were once famous adventurers. Despite Huey's claims that their family is mundane, Webby dismisses this and offers to take the boys to the manor's "wing of secrets". Meanwhile, Scrooge reflects nostalgically on his past endeavors and remarks to Beakley how discontent he is due to the past problems he had with his family over his years of obscurity. Eventually, taking his nephews' inquisitive remarks to heart, he decides to take the boys to the lost City of Atlantis.
As the children enter the wing, they discover it is filled with artifacts and statues. Although the boys become increasingly convinced that the rumors behind Scrooge were true, Dewey comes across an old portrait depicting Scrooge fighting alongside Donald; because they doubt Donald was an adventurer, they conclude that Webby's claims were false. Just then, the kids stumble across a few artifacts that release ancient horrors - the Deus Excalibur, Captain Peghook the pirate ghost, and the Headless Man-Horse - that proceed to team up and attack them. Scrooge arrives on the scene and defeats the ghosts one by one. Despite the children's relief, Scrooge reveals that the wing was actually a garage, and is furious over the trouble they have caused while displaying regret towards spending time with his nephews. When Dewey mocks how spiteful Scrooge is towards family, an infuriated Scrooge tells them to leave.
In his anger however, Scrooge accidentally hits the Gong of Pixiu, which releases the gold-hunting dragon imprisoned inside it. The Pixiu then flies off towards the largest gold storage in Duckburg, which happens to be the Money Bin. Scrooge grabs on the dragon to slow it down; on ground, the children feel guilty for their behavior and decide to help Scrooge. With the help of Launchpad, they rescue Scrooge just as the dragon shakes the duck off. As the kids swing him down from the aeroplane, Scrooge manages to touch the dragon with the Medusa Gauntlet before it can reach the gold, turning it back to stone. Back on the ground, Scrooge berates the nephews for disobeying him, since their antics released the evil entities from his artifact collection and almost killed him, and despite being angry at the kids at first, Scrooge admits to the kids that he enjoyed it and is motivated to restart his adventurer career. His spirit rekindled, Scrooge decides to take them all on a mission to find the Lost Jewel of Atlantis, an immense source of power. Elsewhere, Donald has his job interview and is hired as a sailor by Scrooge’s rival, Flintheart Glomgold, who also seeks the jewel.
During the voyage undersea, Dewey is irritated about Scrooge's cautious measures on keeping the group out of danger. He comes to believe that Scrooge doesn't consider the children, particularity Dewey, as explorers. On the water's surface, a tanker carrying Glomgold's group (consisting of himself, Donald, and mercenaries Gabby, Hack and Slash) detect Scrooge's submarine. Donald discovers that Scrooge and the boys are on board the submarine, and threatens to punish them once he finds them; Glomgold misinterprets Donald's words for actual threats and agrees to this plan as he decides to follow the submarine down to the city. After passing through several underwater obstacles due to Dewey tampering with the map, Scrooge’s submarine reaches Atlantis. They discover that the city is upside-down since the city had collapsed on its own support structure, and begin exploring.
When Glomgold's group arrives after them, Donald realizes that Glomgold could kill his family when he gets the chance. He secretly hinders the attempts on their lives and convinces Glomgold to spare Scrooge so that they can torture him later, to which Glomgold agrees. Due to Dewey’s overeagerness, he tries to cross a bridged boobytrapped with flame throwers as Donald tries to protect him from ruins' trap. When Scrooge tries to go after him, they end up getting separated from the others as the flames finally burn the bridge apart. They watch Glomgold overhead reach the chamber and claims what appears to be the Jewel of Atlantis.
Dewey notices Donald within the group and confronts them believing that Glomgold had his as a hostage. Scrooge pins down Glomgold, and after a brief exchange Glomgold admits that he was using Donald to get close to Scrooge and has his henchmen hold Donald hostage, forcing Scrooge and Dewey to let the evil duck to escape with the jewel. Glomgold then has Gabby throw her sai the 'top' causing the room to flood with water as the trio are trapped inside to drown. As Donald futilely tries to plug the holes, he blames Scrooge for recklessly endangering his nephews to rekindle his adventuring spirit, comparing their situation to a past incident with the Spear of Selene, to which Scrooge denies responsibility. Dewey realizes his overeagerness has endanger Scrooge and Donald and tries to apologize for his action; he then realizes that the jewel Glomgold took was fake as the room was still fully powered and sees the real jewel is right above them. Dewey grabs the jewel with Scrooge and Donald’s help, stopping the water flow. In the commotion, Glomgold leaves his lackeys behind to escape with the jewel. The trio regroups as they find the rest of the team defeating Glomgold’s henchmen. In his submarine, Glomgold fires missiles at Atlantis, causing the city to crumble; however, everyone (including Glomgold's henchmen) escape in Scrooge's sub before Atlantis is destroyed. Back in Duckburg, Glomgold is attending a meeting with the press over how he has uncovered the Jewel of Atlantis. However the press is interrupted when Scrooge arrives with the real jewel and offers to use it as a power source for the city. The media celebrate Scrooge’s return to adventuring, while Glomgold suffers the curse of his jewel by getting caught by a massive tentacle.
Seeing the boys' responsibility and how well the boys bonded with their uncle convinces Beakley and Donald to allow the children to accompany Scrooge on further expeditions. At that moment, Donald's houseboat explodes due to Dewey's earlier mishap, so Scrooge offers to let them all move in McDuck Manor. While Donald has his boat moved into the manor's pool, Scrooge and the kids reorganize the garage's artifacts. Dewey comes across the portrait from before and notices a tear covering a female duck fighting with Scrooge and Donald in the scene, whom Dewey recognizes as his mother.
- David Tennant as Scrooge McDuck
- Danny Pudi as Huey Duck
- Ben Schwartz as Dewey Duck
- Bobby Moynihan as Louie Duck
- Kate Micucci as Webby Vanderquack
- Beck Bennett as Launchpad McQuack
- Toks Olagundoye as Mrs. Beakley
- Tony Anselmo as Donald Duck
- Keith Ferguson as Flintheart Glomgold/Captain Peghook
- Kari Wahlgren as Roxanne Featherly
- Marc Evan Jackson as Bentley Buzzard
- Jennifer Hale as Gabby McStabberson
- Jason Marsden as Hack Smashnikov/Donald's GPS/Babysitter
- Sam Riegel as Slash Smashnikov
- If one counts the original series, this makes fourth DuckTales story to premiere as a TV movie, after "The Treasure of the Golden Suns", "Time is Money", and "Super DuckTales".
- St. Canard from Darkwing Duck, Spoonerville from Goof Troop and TaleSpin's Cape Suzette are all mentioned in the special.
- Webby's bulletin board contains several easter eggs:
- A piece of paper with "F.O.W.L." written on it.
- A crudely drawn picture of Webby wearing pink clothes like her original counterpart.
- Webby's doll from the original show with an arrow through its chest.
- Pictures of Hortense McDuck, Gladstone Gander, Quackmore Duck, Downy McDuck and Fergus McDuck.
- A newspaper clipping reporting on Terra-Firmians.
- Dismal Downs, the home of the McDuck clan, is also written down.
- The theme song plays half an hour in.
- After crossing the boobytrapped bridge in Atlantis, Scrooge tells Dewey to "work smarter, not harder, lad!". This is the same iconic advice that Scrooge's father, McPapa, gave Scrooge in the original series' episode "Once Upon a Dime".
- The Deus Excalibur was likely named after the Latin phrase "deus ex machina", which has come to mean a plot device that suddenly or even abruptly solves a problem.
- Among Scrooge's treasures is possible to see references to the original show. These include:
- Both the blue and black versions of Donald's sailor outfit appear - the blue version was shown to be his casual wear, while the black version came from his temporary employment with Glomgold.
- The painting of Scrooge, Donald, and Della fighting Peghook and his pirates depicts Donald wearing a suit with identical colors as the one Glomgold gave him, meaning he's owned at least two such outfits in his life.
- The second half also airs individually under the title "Escape to/from Atlantis".