One morning, Scrooge is enjoying a cup of tea at McDuck Manor when Della enters his office and directs his attention out the window. To his horror, golden replicas of the Spear of Selene are descending upon Duckburg as the Moonlanders invade the planet Earth. On a news report from Roxanne Featherly, Fenton Crackshell-Cabrera in his Gizmoduck suit and Officer Cabrera approach one of the crafts. Gizmoduck's attempt at a friendly greeting is met with hostility as the Moonlanders attack, with the city quickly falling to their domination.
Scrooge, Della, and the kids manage to reach the Money Bin, only to learn from Gyro that the Moonlanders have taken out all their contingency plans. Lunaris then broadcasts to the city, declaring the Moonlanders' superiority as he seemingly lands a massive ship atop Killmotor Hill. Knowing that the boys are among his targets, Scrooge and Della secretly agree to get them to safety. While Gyro sends Lil Bulb and several duplicates to gather allies from across Duckburg, Della takes the kids in the Cloudslayer on the pretext of recruiting allies from around the globe.
Though the Moonlanders have rounded up most of the citizens, Scrooge is able to gather a motley collection of allies: Beakley, Launchpad, Johnny and Randy, Gabby McStabberson, Duckworth, Gyro, Manny, Gizmoduck, Officer Cabrera (who reveals her knowledge of her son's identity), Lena, Violet, Emily Quackfaster, and Drake Mallard in his Darkwing Duck guise. After a few harebrained proposals, Scrooge marshals his troops into an assault on Lunaris' flagship above Killmotor Hill. Meanwhile, the Cloudslayer nears the Temple of Toth-Ra, only to find it under siege with Amunet and Faris Djinn leading the defense. Della, unwilling to risk the children's safety, flies away, but the kids are inspired by the defeat of Toth-Ra and set course for Ithaquack.
Back in Duckburg, Scrooge leads his forces into battle, and charges ahead with Launchpad and Darkwing while the others hold off the Moonlander guards. The heroes call in additional allies, including the Harpies and several clones created by Gyro. Arriving at Ithaquack, the Ducks learn that Zeus has grounded Selene and Storkules, and refuses to allow the group in despite Della's pleas. As the kids question Della's actions, a Moonlander ship arrives to attack, forcing them to flee in the Cloudslayer.
In Duckburg, Scrooge switches outfits with Darkwing, who with Launchpad deals with security on the lawn of McDuck Manor. Scrooge infiltrates the manor itself, and gets to the entrance ramp of Lunaris' ship only to find that it's a giant hologram. Lunaris then reveals that he predicted Scrooge's actions, and demonstrates the capture of most of Scrooge's allies and the Cloudchaser being shot down. He then lands his true flagship, a Planetary Engine designed to cause the Earth to begin orbiting the moon.
Della and the kids find themselves stranded on an apparently deserted island, only for Donald—scruffy and accompanied by a ventriloquist dummy melon who mysteriously resembles a popular mouse; to emerge from the undergrowth.
Donald and Della, recognizing each other, are initially furious, Della for Donald's long absence and Donald for Della not getting his message. Dewey breaks it up then gets mad at Donald saying he owes him 11 years of Turbo. Then the two siblings embrace, and the kids are quick to conceal the fact that they were unaware of Donald's going missing. However, when they suggest finding a way back home, Della admits that she took the kids away from Duckburg to keep them safe. Meanwhile, Duckburg begins to freeze over due to Lunaris' engine moving the Earth, and Scrooge assembles at Chum's with Beakley, Manny, Launchpad, and Duckworth, his last remaining allies.
Duckworth soon ditches the group and heads to the afterlife to "prepare places for them", while Scrooge is at a loss as to how to defeat Lunaris. Unlikely—and unwelcome—help appears in the form of Flintheart Glomgold, whom Scrooge realizes may actually be the key to victory. Back on the island, Della attempts to convince her family to stay on the island, but upon realizing that she feels stranded as she was on the moon kicks Donald's melon into the ocean in a rage. Louie then approaches her and, after rekindling her fighting spirit with her lullaby (which Donald shared with the boys), the Ducks are startled by some unexpected arrivals: Fethry, Gladstone, and Mitzy with the Gladyear Blimp.
Back in Duckburg, Scrooge and his few allies put up with Glomgold's inane plans, having no real alternatives. The scheme calls upon Beakley—dressed as a child—to operate a giant slingshot to fire Launchpad—dressed as a rock—into Lunaris' flagship. Having dressed several of his pet sharks in parkas, Glomgold sends them in under the iced over Audobon Bay to attack the supports of Lunaris' ship. Much to Scrooge's chagrin, he is sent to distract Lunaris by driving a Manny-drawn sleigh...dressed as Santa Claus.
After catching up, Fethry and Gladstone carry their cousins and the kids back towards Duckburg aboard Mitzy. In Duckburg, Lunaris catches on to Glomgold's plan and is baffled, particularly as Scrooge and Glomgold begin quarreling in front of him. As the sharks and Launchpad accomplish their task, the two rivals and Manny engage Lunaris in a hand-to-hand battle. Despite their brave efforts, Lunaris emerges on top, only for Mitzy to arrive and join in the attack.
Gladstone's luck helps take out the last support holding up Lunaris' Planetary Engine, which begins to tumble as Lunaris scrambles back inside. Taking advantage of its still active thruster, Mitzy catches the falling craft and aims it back towards the moon. Unfortunately, Lunaris regains the controls and, determined to achieve victory, decides to destroy the Earth if he cannot conquer it by ramming his ship through the core. Seeing this, Della boards a nearby Spear with Donald, Scrooge, and the kids.
With the kids acting as gunners and Donald and Della fighting over the controls, the Ducks attempt to halt Lunaris' flagship. Unfortunately, his final line of defenses proves too much, and all hope seems lost. Luckily, Penumbra then appears in the original Spear of Selene and crashes into Lunaris' last engine, crippling his ship, and is picked up by Della and her family. Glomgold's sharks have eaten away at the ship's circuitry and Selene then appears on Lunaris' bridge and informs him, to his dismay, that not only has Storkules gotten Earth back into orbit, but his flagship has become a second moon.
Back on Earth, the freed citizens of Duckburg and the heroes gather in celebration of their victory. Launchpad becomes smitten with Penumbra, and the Ducks are confident that they can face any future difficulties as a family. Unbeknownst to them, they are being observed by the Board of Directors, who prove to be the High Command of F.O.W.L. Having grown tired of Scrooge and his family threatening their schemes, the group—including Gandra Dee, Jeeves, a cryo-frozen Rockerduck, Steelbeak, the Phantom Blot (disguised as a Funso mascot), and Black Heron—set out to eliminate them once and for all.
- 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
- Paget Brewster as Della Duck
- Tony Anselmo as Donald Duck
- Toks Olagundoye as Mrs. Beakley
- Lance Reddick as General Lunaris
- Julie Bowen as Penumbra
- Jim Rash as Gyro Gearloose
- Lin-Manuel Miranda as Fenton Crackshell
- Libe Barer as Violet Sabrewing
- Kimiko Glenn as Lena
- Chris Diamantopoulos as Darkwing Duck, Storkules, Melon
- Selenis Leyva as Officer Cabrera
- Marc Evan Jackson as Bradford Buzzard
- Paul F. Tompkins as Gladstone Gander
- Tom Kenny as Fethry Duck
- April Winchell as Zenith
- Rob Paulsen as Gibbous
- Laura Bailey as Palus
- Michael Chiklis as Zeus
- Nia Vardalos as Selene
- Omid Abtahi as D'jinn
- David Kaye as Duckworth
- Cree Summer as Amunet
- Susanne Blakeslee as Miss Quackfaster
- Kari Wahlgren as Roxanne Featherly
- Keith Ferguson as Flintheart Glomgold, Moonlander Mascon
- As a Hidden Mickey (if you can call it hidden), Donald is seen holding a watermelon that is shaped like Mickey Mouse's head and has his voice.
- Chris Diamantopoulos reprises his role as Mickey for this cameo, but as Mickey's character rights were not included for DuckTales, it is listed in the credits as "Melon" instead, though the subtitles list it as “Mickey”.
- When Donald and the melon first appear, the melon "says" "Hot dog, we got company" a reference to Mickey's first speaking appearance, "The Karnival Kid", which featured the line "Hot dog, hot dog" as Mickey's first words.
- When Della kicks the melon into the sea, it "screams", "See ya real soon!", Mickey's signature closing line, originating from The Mickey Mouse Club.
- Donald's appearance is a reference to Tom Hanks' 2000 drama film Cast Away, with Melon Mickey serving as his Wilson.
- Gizmoduck's line when he introduces himself to Darkwing "When there's trouble you call me" is a spoof of the lines from the Darkwing Duck theme song, "When there's trouble you call DW".
- When battling the Moonlanders, Scrooge orders his troops to hold position no matter what, using the same kind of strategy used by William Wallace in the film, Braveheart, who, like Scrooge, is Scottish.
- When Scrooge's army faces the Moonlanders, Scrooge at the beginning of the battle attacks the Moonlanders with his cane by first bouncing off their heads, and then swinging it to deflect a blast back to them. These moves are a throwback to the moves Scrooge used in the DuckTales, DuckTales 2, and DuckTales Remastered video games that were produced by Capcom.
- While introducing himself, Darkwing Duck refers himself as "the scream you can hear in space", a clear reference to the tagline of the Aliens franchise: "In space, no one can hear you scream".
- The individual episodes are titled "Moonvasion! Part I" and "Moonvasion! Part II" for episode reruns.
- This is the final episode aired on Disney Channel before the series moved back to Disney XD.