The moon invades Duckburg, forcing Scrooge to join forces with an unlikely ally in an effort to save Earth. Meanwhile, Della and the kids search the globe for reinforcements.
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 approaches one of the crafts and offers a Moonlander a pie as a peace offering. However, Gizmoduck's attempt at a friendly greeting is met with hostility as the Moonlander fires her weapon straight towards him, but Officer Cabrera saves him by shoving him to the ground. Immediately after the attack, further Moonlanders exit the ship and begin terrorizing the citizens, with the city quickly falling to their domination.
Scrooge, Della, Beakley, and the kids manage to reach the Money Bin by driving, but Della is flabbergasted about the invasion due to the Moonlanders coming off as nice when she last met them. Once inside, Scrooge orders Gyro to prepare his contingency plans, only to learn from Gyro that the Moonlanders have already disabled the plans, while acknowledging how thought out the invasion truly is. Lunaris then broadcasts to the city, declaring the Moonlanders' superiority as he seemingly lands a massive ship atop Killmotor Hill. Hearing 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 as a hidden transmission method to gather allies from across Duckburg, Della takes Webby and the boys on a plane ride with the Cloudslayer on the pretext of recruiting allies from around the globe.
During which time, Launchpad attempts to flee from the Moonlanders with his broken car, but is saved by Darkwing Duck, as they then receive the Bulb message and move towards the Bin. Gizmoduck receives the message while helping citizens escape wreckage, Lena receives it while avoiding Moonlanders within a playground, and Mrs. Quackfaster and Violet receive it while hiding within the Duckburg Public Library. However, the secret gathering is nearly foiled when Moonlander Gibbous catches one of the Bulbs, but it destroys itself before anymore information is said aloud.
Although the majority of Duckburg's citizens are captured, further allies who receive the message include Beakley, Johnny and Randy, Gabby McStabberson, Duckworth, Gyro, Manny, and Officer Cabrera (who reveals to Fenton her knowledge of her son's identity as Gizmoduck) as they then hold a meeting within the Money Bin. 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. Although they prove a good fight, they're still forced to retreat back into the pyramid. 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. Beakley uses her martial arts skills to proceed the attack, Duckworth uses his Demonworth form to assist in the fight, Lena and Violet fend off the Moonlanders with their magic abilities, and Gabby and Quackfaster use their sword skills to disarm the Moonlanders. As officer Cabrera fights along side Gizmoduck, she encourages her son to cream the Moonlanders using his Lemon Meringue pies, which then attract Harpies to attack them.
Gyro and his clones also attempt to assist in the fight, but the majority of the clones disintegrate from the attacks (and possibly the real Gyro as the clones aren't sure who the original one is). Meanwhile as the Ducks arrive at Ithaquack, they learn that Zeus has grounded Selene and Storkules, and refuses to allow the group in despite Della's pleas. Storkules pleas to his father to let him help, but is instead electrocuted with his father's lightning bolts. As the kids question Della's actions, a Moonlander ship arrives to attack, forcing them to flee in the Cloudslayer.
As Della searches through the map while flying above the ocean for abandoned places her and the kids can hide, Webby reminds her that their "plan" isn't working. Louie ultimately sees through the ruse: Della isn't trying to look for help, she's running away from the battle and is taking the kids with her. With Della distracted while admitting she isn't willing to lose them again, the Moonlander ship returns and the Cloudslayer gets shot down.
In Duckburg, Scrooge switches outfits with Darkwing in order to seem like less of a threat, with Launchpad dealing with security along side Darkwing, now dressed in Scrooge's clothes to mislead the Moonlanders by targeting him instead on the lawn of McDuck Manor. Scrooge infiltrates the manor itself while dealing with poorly Moonlander soldiers Gibbous and Zenith. However, once he gets to the entrance ramp of Lunaris' ship, he realizes he fell into a trap after discovering the ship is a giant hologram. Lunaris then reveals through a holographic screen that he predicted Scrooge's actions, and demonstrates the capture of most of Scrooge's allies and the Cloudslayer being shot down. He then lands his true flagship stationed in front of the Marina, a Planetary Engine designed to cause the Earth to begin orbiting the Moon, much to Scrooge's absolute shock.
Once the Cloudslayer crashes to the ground, Della and the kids find themselves stranded on an apparently deserted island. Moments later, they discover Donald—scruffy emerging from the undergrowth, accompanied by a ventriloquist dummy made of melons he named Melon.
Donald and Della recognize each other, as they then approach one another in a friendly manner, but then, both shout in a fit of rage when losing their tempers. Della yells at Donald for his long absence while noting that an invasion is currently happening, and Donald yells at Della for him having already been aware of the invasion prior while claiming he tried to warn them. Dewey originally breaks the fight up, but he then gets mad at Donald due to his recent realization that he could've been named Turbo instead of Dewey, so he grabs Donald's beard while claiming he owes him 11 years of Turbo before Della pulls him out of the way. Although the two siblings are furious at another for having been apart for so long, they tearfully embrace once they admit how much they really missed each other.
However, the hug is cut short once Della begins to feel creeped out over Donald's voice mimicking for Melon. 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. Back On the island, Melon explains that Della's Moonlander roommate Penumbra helped Donald escape from Lunaris after he accidentally landed himself on the Moon, where he then crash landed on the island and was unable to call for help.
Although Donald believes they were searching for him the last couple months, the kids are quick to conceal the fact that they were unaware of Donald's predicament, as they believed he was still on his cruise trip. However, when Donald suggests finding a way back to Duckburg to help Scrooge, Della admits that she took the kids away from Duckburg to keep them safe. Wanting to keep it that way, Della claims Scrooge would know what he's doing for the battle. Back in Duckburg with Scrooge still clueless on a plan, an unlikely—and unwelcome—help appears in the form of Flintheart Glomgold, who claims he has a plan of his own.
Although Beakley points out that the majority of his plans have backfired severely on him in the past, Scrooge is forced to listen after realizing he has no good ideas left. Back on the island, Della attempts to convince her family to stay on the island by refurnishing the Cloudslayer, but everyone is still keen on figuring out a way to leave. Even with the group constantly questioning her planned adaption to staying, she still tries to convince them it's fine. But once Dewey points out their current predicament as similar as being back on the Moon, Della begins to lose her sanity.
On the other hand, once Della instinctively suggests they have some oxy chew, she realizes it really is like the Moon and kicks Melon into the ocean out of rage. Back in Duckburg, Scrooge and his few allies put up with Glomgold's inane plans and immature slideshow, having no real alternatives. But when Glomgold introduces them to a shark wearing a coat for his plan, Scrooge begins to lose faith in Glomgold. Back on the island, Louie approaches Della within the cloudslayer while she is hanging up the picture she drew on the Moon of Huey, Dewey and Louie.
He then has a heart-to-heart talk with her as she admits all she ever thought about on the Moon was the fun and amazing adventures she wanted to have with them, but her new life as a mother proved to be more difficult than she thought. Louie assures her that it's always great to find a right angle to take control of a situation, but you simply can't plan for everything. He also believes that while you're bound to deal with bad surprises, they may also lead to a good one. Louie then recalls a song he sang to himself when he was young every time he felt scared, which Della recognizes it as her own lullaby she sang to them before they hatched. Louie then claims Donald used to sing it to them when they were little, with Donald himself adding that he sung it every night. This gives Della the confidence to face the unknown together, but she and the others still unsure on how to get back to Duckburg.
Suddenly the Ducks are startled by some unexpected arrivals: Fethry, and Gladstone, who are seen riding on top of Mitzy with the Gladyear Blimp attached to her. Gladstone then explains that just before the Moonlanders attacked Duckburg, his Blimp had luckily been blown away out to sea, where he ran into Fethry and Mitzy along the way. During the trip, he then spotted some melons floating around in the ocean, which brought them to the island Donald, Della and the kids are currently on. During which time, Gladstone is eating one of the melons they found, shocking Donald after realizing he is eating his friend Melon. After further preparations, Fethry and Gladstone carry their cousins and the kids back towards Duckburg aboard Mitzy.
Back in Duckburg, Glomgold calls upon Beakley to dress as a little boy to maintain the illusion while operating a giant slingshot. Launchpad places himself into a sphere shaped like a rock, which Beakley can then use the slingshot to send him into Lunaris' ship with the hopes of shutting down the engine. 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.
Lunaris catches on to Glomgold's plan through his monitors and is baffled. He then exits the ship and begins to question Scrooge on his embarrassing actions, but while Scrooge is reading from Glomgold's script, Glomgold himself surprises Lunaris by showing himself through the sack of gifts on the sleigh. However, Scrooge and Glomgold begin quarreling in front of Lunaris after Scrooge, as Santa, unwittingly gives Glomgold back his company due to a line he was forced to say through the script. Meanwhile Beakley manages to slingshot Launchpad into one of the control rooms of the mothership, where he destroys part of the controls including part of the rocket engine.
At the same time, Glomgold's sharks successfully weaken one of the ship's supports underwater, distracting Lunaris long enough for Scrooge to disable him from his gun. Scrooge, Glomgold and Manny then engage Lunaris in a hand-to-hand battle, but Lunaris proves to be the better fighter even against all three. He then attempts to make his way back to the ship's entrance, but Manny is able to Launch Scrooge towards Lunaris before he can. The battle continues as Lunaris proclaims his dominance over Earth with the planet Moon, but Glomgold points out that the Moon's not a planet, much to Lunaris' annoyance.
In the end, Lunaris manages to slam Glomgold to the ground hard enough to keep him down, while he shoves Scrooge towards the ship's wall and causes him to take a hard fall. Lunaris then approaches Scrooge once more and asks him for his last words, but as soon as he says that, Mitzy and the gang aboard her arrive right in front of them. Fethry then encourages Mitzy to begin pulling one of the ship's supports in order to destabilize the ship's angle towards the ground. This forces Lunaris leave Scrooge be and flee back into his ship, but Mitzy's strength is still not strong enough to break apart the ship's support.
Regardless, Gladstone's luck comes into play as he drops a slice of melon, which is caught by nearby seagulls, but dropped again in front of Launchpad. This leads the seagulls to attack Launchpad and cause him to unknowingly pull a lever that releases the support Mitzy was trying to pull, as he then falls out of the ship before it begins tumbling over. Taking advantage of its still active thruster, Mitzy catches the falling craft and aims it back towards the moon. Both Scrooge's group and everyone aboard Mitzy share a brief reunion, but during which time Lunaris regains control of the ship.
Determined to now achieve victory no matter the cost, Lunaris decides to destroy the Earth if he cannot conquer it by rotating it around the moon, which the other Moonlanders hear and realize they are the bad guys. Seeing this, Della spots a nearby invasion ship and boards it with a small crew consisting of Donald, Scrooge, Huey, Dewey, Louie, and Webby. They then fly the ship into space in order to stop Lunaris from going through with his evil plan.
With Scrooge acting as the commander, the kids acting as gunners and Donald and Della fighting over the controls, the Ducks attempt to halt Lunaris' mothership. Through brief avoidance of Lunaris' laser turrets, Della ultimately takes full control over the ship and flies it straight up, as she then dives down towards the top surface of Lunaris' ship to disable his turrets. She then makes a U-turn and heads beneath the ship while destroying further turrets, as they then approach the back of the ship to destroy Lunaris' thruster engine. Unfortunately, this proves to be another trap by Lunaris as he then activates hidden laser turrets surrounding the thruster. The group's lasers were then shot, as Della tries to fly their ship away but every time she tries, their ship only gets more and more damaged.
Knowing they were now trapped, Lunaris increases his thruster's power in order to overheat their ship and inevitably cause it to be destroyed. However, just as Lunaris is about to proclaim victory, another ship on his radar appears on alert and is seen coming his way. Penumbra then appears in the original Spear of Selene and crashes into Lunaris' thruster, crippling his ship. Although the Spear of Selene is destroyed, Penumbra luckily survives the explosion and is picked up by the family with their invasion ship, as they fly into the Earth's orbit and make their way back to Duckburg.
Meanwhile Lunaris attempts to activate his ship's backup engines, only to realize Glomgold's sharks have eaten away at the ship's circuitry. Selene then appears in front of him and informs him, much to his dismay, that not only has Storkules gotten Earth back into orbit with his strength, but the mothership he is aboard has now become the Earth's second moon. Back on Earth, the freed citizens of Duckburg and the heroes gather in celebration of their victory, after the Moonlanders release them all from their capture once realizing their leaders evil intentions. While Launchpad becomes smitten with Penumbra, Scrooge becomes annoyed with Glomgold after claiming he defeated Scrooge to everyone, even though they were on the same team. In the end the Ducks grow confident that they can face any future unknown difficulties as a family, as they and their allies join together for one final group shot.
Unbeknownst to them, they are being observed by the Board of Directors, who prove to be the High Command of F.O.W.L. The meeting also consists of Gandra Dee, Jeeves, a cryo-frozen Rockerduck, Steelbeak, Phantom Blot (disguised as a Funso mascot), and Black Heron. The Board of Directors then claim the pieces are now in place, and that it's time for them to step out of the shadows. Having now grown tired of Scrooge and his family threatening their schemes through their adventures, they now intend to give the family their last adventure ever.
Scrooge references his great-grandfather. He also paraphrases the Scottish proverb: "Twelve Highlanders and a bagpipe make a rebellion." but in a sort of General Douglas MacArthur manner: "Give me ten thousand Filipinos and I shall conquer the world!"
Donald's melon, besides being an obvious reference to the Tom Hanks film, Cast Away, is in the shape of Mickey Mouse; this is further emphasized by it being "voiced" by Chris Diamantopoulos, one of Mickey's current voice actors, and its use of several of Mickey's signature phrases.
Upon finding Donald with Mickey Mouse's head made out of a melon on an island, Donald tells them in Mickey's voice: "Hot dog, we got company". This is a reference to Mickey's very first lines from The Karnival Kid.
As the watermelon of Mickey Mouse's head gets tossed into the sea, Donald says to it: "See you Real Soon", which is the closing line of each episode in The Mickey Mouse Club and House of Mouse.
Close captioning identifies the melon as Mikey often showing the "Mikey's Voice" tagline whenever Donald speaks as him. Although it could be a typo for the name Mickey, it does show that the Mickey Mouse and Melon connection was intentional.
A rendition of the Moon Stage Theme can be heard during the duck family and Lunaris spaceship battle.
Dewey revealed that he and his brothers are eleven years old; the triplets' age had never been mentioned specifically before now. However, Scrooge noted in "The Last Crash of the Sunchaser!" that the boys were hatched shortly after Della's disappearance, and various episodes indicated that Della was trapped on the moon for approximately ten years.
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.
Glomgold pays tribute to Shaw from the film, Jaws when he scrapes his fingers across a whiteboard, who did the same kind of thing in his scene of introduction.
When Scrooge poses as Darkwing Duck, this pays tribute to the episode "The Masked Mallard" of the original DuckTales when Scrooge took on the identity of the titular superhero, a name of which would later become one of Darkwing's Superhero Sobriquets in Darkwing Duck.
This is the final episode aired on Disney Channel before the series moved back to Disney XD.