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Part 1: "Marking Time"
The serial opens up with Scrooge McDuck attempting to purchase the westernmost of Flintheart Glomgold's island chain, Duckbill Island. Glomgold refuses to accept less than $20,000,000. Scrooge reluctantly hands over $10,000,000, and promises the other half by noon on Friday or he'll lose his down payment and his purchase according to Glomgold. Huey, Dewey and Louie are eager to know why Scrooge is wasting millions of bucks on the seemingly worthless piece of land. Scrooge explains that he came upon a cave while exploring the island full of skeletons, cave drawings and very large diamonds. But Glomgold spies on them and is upset that he was tricked out of his very own diamond mine. He calls the Beagle Boys and orders them to plant dynamite around the cave while Scrooge and the nephews sleep. When Scrooge awakens, Flintheart and the Beagles show up to tell them that what now remains outside the cave is now the westernmost island that Scrooge bought, and Flintheart now owns Duckbill Island's diamond-infested cave.
Scrooge turns to Gyro Gearloose for help. Fortunately, Gyro has discovered a new element called bombastium, which looks like a glow-in-the-dark popsicle, and has the ability travel through time. In light of his discovery, Gyro built a bombastium-powered helicopter called the Millennium Shortcut, with controls designed to be flown by Launchpad McQuack. Taking along a laser disguised a pen, Scrooge, Launchpad, and the boys attempt to head back in time to before the explosion. Unfortunately, a near run-in with a plane causes Launchpad to spin the helicopter's timeclock continuously, inevitably sending the group farther back in time than anticipated.
The group arrive on Duckbill Island as it was 65 million years ago. Here they run into a caveduck named Bubba, whom they accidentally save from becoming lunch for a Tyrannosaurus Rex. Scrooge is upset with ending up in prehistoric times, and he doesn't take kindly to Bubba, who is devoted to "Skooge" (as he calls him) for saving his life. Bubba then takes Scrooge to his cave, which coincidentally turns out to be the future diamond mine. Scrooge gets the idea to leave his marker all over the cave to prove that he legally owns the diamond mine and to wrestle it away from the clutches of Glomgold. Scrooge attempts to use his laser pen to mark a nearby rock which turns out to be Bubba's pet Triceratops and accidentally burns the dinosaur, who steps on Launchpad's foot. Bubba later names her Tootsie, after Launchpad's foot. The group stumble upon a priceless skeleton of a Rogetthesaurus. As Launchpad loads the skeleton into the time machine, Scrooge proceeds to leave his "money" signature throughout the cave, while the nephews introduce Bubba to music.
The time machine's freezer busts and the bombastium starts to melt. Bubba and the nephews wander off and just as Scrooge and Launchpad find the boys, they return to find the Millennium Shortcut missing. Bubba, now an honorary Junior Woodchuck thanks to Huey, Dewey, and Louie, helps the group track the machine down. They find the machine in the hands of the magenta T-Rex who earlier tried to eat Bubba. In a complicated process, the heroes distract "Jerkzilla" as Scrooge calls him, away from the plane, using taunts and banana peels.
Huey, Dewey, and Louie want to take Bubba and Tootsie with them, but Scrooge would not have it, as he views Bubba as more of a pest. But as the Millennium Shortcut takes off, the T-Rex returns, angrier than ever. He bites at the machine's landing gear, preventing them from leaving. The heroes believe the weight of the Rogetthesaurus bones are preventing them from taking off, and after some convincing from the nephews, Scrooge reluctantly jettisons them, hitting the T-Rex. During this, Bubba attempts to help the time travelers by clubbing the T-Rex on the head as the bones are being dumped, but he unintentionally stows away on the plane with Tootsie. Scrooge balks and blames the prehistoric passengers for the stalled take-off and the loss of his $1,000,000 skeleton. But before Scrooge can take them back, Launchpad pilots them through time once more.
Part 2: "The Duck Who Would Be King"
After a crash landing, the Millennium Shortcut's controls are jammed, so Scrooge and Launchpad set out looking for help. What they find is Tupei, "a 14-karat mirage" where a sinister tyrant named Mung Ho is about to execute an innocent girl named Sen-Sen for her beliefs that he is an impostor and that "the Great One" is coming. According to Sen-Sen, the prophecy states "Good will win when iron walks and gates give forth a blizzard and we shall see the Great One ride atop a giant lizard". As the two hide in a giant statue, Launchpad admires Sen-Sen's beauty and he blows their cover by defending her. Mung prepares to execute Scrooge and Launchpad as well, but Bubba arrives riding atop Tootsie. This astounds and nearly convinces the crowd that Bubba is the so-called "Great One". Mung tries to convince Bubba to let him continue with his tasks, but Bubba, because of his affection for "Skooge", puts him in charge instead. In a running gag, all the townsfolk address him as "Skooge" also. ("That's Scrooge!" "Whatever.")
Scrooges tells the citizens to go fetch Bubba's "flying chariot", and that Sen-Sen be set free. As she escorts them to Bubba's new palace, Scrooge tells Sen-Sen that as soon as the Millennium Shortcut returns, they will leave much to the reluctance of Launchpad. Sen-Sen insists that they stay as the she believes the prophecy has not yet been fulfilled. The villagers return with "the flying chariot", and the group realize the bombastium has melted potentially trapping them in time. The nephews suggest they take the liquid bombastium to the snowy mountains in the horizon to re-freeze it.
As Launchpad and the boys set out for the mountains, Scrooge mutters about in boredom until Sen-Sen shows him the treasure room, which resembles Scrooge's Money Bin in Duckburg. Feeling nostalgic, Scrooge swims and burrows around the wealth until Sen-Sen tells him that these are treasures Mung Ho took from the people in the name of the Great One. Scrooge takes Bubba with him to talk with Mung Ho. Scrooge with the approval of the "Great One", calls a trial with Mung Ho as the defendant; the tyrant watches in horror as everything he's taken is ordered by Bubba to be given back to the people. Mung Ho then reminds them that every year at this time the bandits return and now he will no longer be here to defend the city. But as it turns out, the bandits work for Mung Ho and he was paying them in previous years to fake sieges of the city. This time he orders them to "ransack the city and destroy Skooge so that heads will roll in Tupei!"
Scrooge, meanwhile, did not think either he or Bubba can defeat the marauders until he remembers the laser pen in his possession. In the meantime, Launchpad, Huey, Dewey, and Louie head up the snowy mountain. While the boys wait for the bombastium to freeze, Launchpad carves a monument of Sen-Sen in the snow. As he is about to leave, he ends up tipping the duckbill of his monument causing a giant snowball to come rolling down, taking him, the boys, and the refrozen bombastium with it. Back at the palace gates, Scrooge dons ancient armor and proceeds to face off against Mung Ho and his band of marauders. Among the cutthroats was a giant wielding a scimitar that demonstrates his strength by cutting a boulder in half. Scrooge counters the feat and instills fear in the thieves by slicing down nearly everything in sight with his laser. Unfortunately, the laser pen runs out of "ink" and the giant marauder capitalizes on this by knocking Scrooge out and prepares to finish him off with a stomp. But Bubba, club drawn, intervenes to help Scrooge and clobbers the giant down. As Bubba carries Scrooge back through the gates, Mung Ho orders them to be knocked down. Just then, Launchpad, Hewey, Dewey, and Louie come rolling in their giant snowball knocking down the gates and a few cutthroats, fulfilling the "gates give forth a blizzard" prophecy.
Mung Ho whines for his minions to destroy everyone, but Launchpad leads the gang into a secret hatch he had found earlier, hidden in the statue. His operation of the iron statue scares off Mung Ho's army, and eventually Mung Ho himself, completing the prophecy with "the iron walks". Later, as our heroes prepare to leave, Scrooge turns over leadership reigns of Tupei to Sen-Sen, who reminds him that it was Bubba "the Great One" who defeated the giant while Scrooge lay senseless. She also shows Launchpad her way of saying goodbye by planting a big kiss on him. As the travelers depart, the Tupei citizens finally get Scrooge's name right, to which Scrooge replies, "That's Skooge! ...Whatever."
Part 3: "Bubba Trubba"
Our heroes finally arrive back in their own time, right after the moment they left. While Bubba is fascinated with modern inventions, Gyro realizes there may be timeline-changing trouble rising from this development; Scrooge tells Gyro to fix up the Millennium Shortcut so they can send "that prehistoric pest" back where he came from. Scrooge and the nephews arrive back at the McDuck Mansion with Bubba and Tootsie in tow, and Scrooge tells his staff that he's going to tell the world that he's outfoxed Flintheart Glomgold by introducing Bubba and his new legal markers in the diamond mine cave on national TV. Needless to say, this upsets Glomgold and he hatches a plan to capture Bubba so that he may turn him against Scrooge destroy those cave markers.
Meanwhile, Scrooge becomes rather irritated with Bubba and Tootsie due to all of the trouble, he attributes, that they are causing him. He pays Gyro a visit, inquiring how long till the Millennium Shortcut will be repaired so that he can send that "neander-duck" home. Gyro tells Scrooge that he potentially created a time paradox when he brought Bubba and Tootsie back with him, possibly big enough to swallow the Money Bin. Scrooge passes the words off as rubbish and tells Gyro he only believes in the stack money he now holds in his hands. But as he says this, a sudden gust of wind blows the currency away. Fearing the worst, Scrooge tells his nephews to watch Bubba, and to also perhaps get him away from Scrooge's money. So Huey, Dewey, and Louie take Bubba to school, where he starts up a sudden song-and-dance number joined by all the students and even the teacher. When the principal see this, he sends Bubba away and makes the nephews stay after school. As Bubba reluctantly heads home, the Beagle Boys try to capture him, but are unsuccessful as their plan backfires.
Back at the McDuck mansion, Scrooge continues to believe that Bubba is the root of all of his problems and proceeds to pawn Bubba off on Mrs. Beakley in hopes that she will now spend time with him. She takes him to the snooty Duckburg Rose Society where once again, the Beagle Boys try to capture him by luring Tootsie into a trap. But once again, the Beagle Boys plans are foiled. As Bubba attempts a rescue, he inevitably creates chaos throughout the party, ultimately resulting in numerous repair bills and the banning of Mrs. Beakley from the Rose Society until May 1999.
After a crafty bribe of a new scarf, Launchpad is the next one in line to watch over Bubba. Again, the Beagle Boys unveil their latest attempt at capturing Bubba when Big Time Beagle disguises himself as an old lady needing help and preys upon Bubba's good will of being a "Junior Woodchuck". The plan fails once more, as he finds a "shiny" coin in the street and decides to "give [it] to Skooge." Launchpad then takes Bubba and Tootsie to the Duckburg Museum, where Bubba mistakes the fake dinosaurs for real-life reptiles and eventually causes more unintentional destruction by wreaking havoc in the museum.
Out of allies in his quest for babysitting Bubba, Scrooge keeps him preoccupied with the job of stopping the drip of his restroom faucets. Scrooge then relaxes by taking a swim in his money and suddenly finds himself talking with his conscience (represented as a tiny Scrooge), who informs him that his troubles will be over once he stops blaming Bubba. But as Scrooge listens, Bubba attempts to stop the drip from a nearby hose which spouts water wildly and in need of help, innocently lets the Beagle Boys inside the money bin. Scrooge opens the vault doors to find the Beagle Boys waiting and faints at the sight.
Part 4: "Ducks on the Lam"
The Beagle Boys waste no time kicking Scrooge, Bubba, and Tootsie out, and then reveal to Scrooge that Bubba was the one who gave them access to the bin. Even after the talk with his conscience, Scrooge is seething with anger and banishes Bubba from his sight. Inside the Bin, the Beagles happily enjoy playing with Scrooge's money and decide to call Glomgold to gloat. Glomgold convinces them that it will be impossible to carry out all of Scrooge's money and that by now Scrooge has called every army in the country. The Beagles Boys, now desperate, ask for aid from Glomgold and he advises them to use the money bin's security systems as defense.
Glomgold then arrives later to mock Scrooge and reminds him that he still owes him $10,000,000 (despite the cave markers in Bubba's cave not being destroyed). Furious, Scrooge orders the army to charge in and retrieve the bin. But with Scrooge being the richest duck in the world, he of course has the best security system money can buy, and all his attempts to get his bin back fail. Scrooge then decides to borrow the required cash from one of his banks. Glomgold eavesdrops and tells the Beagle Boys to pretend to be Scrooge and call all the banks in town claiming that an impostor Scrooge McDuck is running around town claiming to be him. According to the Beagle Boys, the "real" Scrooge will speak in code and reply to "I have fish in my pockets".
After failing to get money from his own banks due to the Beagles' slander, Scrooge returns home and has Huey, Dewey, and Louie help him look for loose change throughout the mansion. Unfortunately, they come up $8,000,000 short and Scrooge decides to try one more bank. When he arrives, he is met with the bank manager and is furious when the phrase "fish in their pockets" is constantly mentioned. Thinking he's the imposter, the bank manager has Scrooge arrested. Meanwhile, a saddened Bubba walks around Duckburg looking for new friends. He initially makes new friends, but his bad luck results in him landing in jail also.
After landing in his cell, Scrooge continues to blame Bubba for all of his troubles. His conscience suddenly reappears and reassures him that it is not Bubba that is the problem but Scrooge himself. At first Scrooge is skeptical, but his conscience reassures him that the real Scrooge McDuck would not blame his problems on fate or little boys. Scrooge then begs for another chance and his conscience reminds him of the money in the diamond mine. Scrooge then ponders a way out of his current predicament and unknowingly tells Bubba to stop Tootsie's bellowing. To his shock, he soon realizes that both Bubba and Tootsie are in the cell next to him. Realizing how cruel he was to blame Bubba for all of his recent troubles, Scrooge tearfully apologizes, vowing to return Bubba home to his home. Bubba responds by giving him the "shiny" he found in the street earlier, which touch Scrooge's heart and shed emotional tears, and, hearing that Scrooge wanted out of his prison, has Tootsie break down the wall.
The trio escape with the police in close pursuit. They finally elude the cops after finding a good hiding spot up high in a lamppost. When Scrooge attempts to call his nephews at the mansion, Glomgold arrives and calls the police. Bubba and Tootsie come to the rescue by suddenly sending the lamppost crushing down on Glomgold. Flintheart gives chase after the cave dwellers as Scrooge tries to get away in a shopping cart. As Glomgold pursues Bubba and Tootsie, Scrooge secretly nabs Glomgold's limousine phone and calls Louie, ending up (unknowingly) with all three of the nephews on the phone. Scrooge then tells them to have Launchpad to ready the plane and have Gyro bring the time machine over.
Over at the mansion, Gyro pushes the Millennium Shortcut over just as Scrooge, Bubba, and Tootsie arrive in the shopping cart crashing into the Mansion's fountain. As Bubba helps Scrooge to his feet, the nephews try to defend Bubba, but Scrooge assures them that he cares for Bubba. Scrooge then tells Gyro to ready the machine to send Bubba home. Hearing this, Bubba does not want to go due to his affection for "Skooge". After some convincing, they say goodbye and Bubba gets in the Millennium Shortcut powered by the last bar of bombastium and travels back through time. The police finally arrive, storming the mansion gates just as Scrooge changes into his normal wear. As Scrooge, Launchpad, and the boys set for Duckbill Island, the cops are angry with Duckworth for letting the supposed impostor escape, but the butler assures them that there was the real Scrooge McDuck.
Part 5: "Ali Bubba's Cave"
The heroes reach Duckbill Island, and Launchpad surprisingly brings them down without crashing. This of course troubles Launchpad, but Huey, Dewey, and Louie, reassure him that he still landed them on the wrong side of the island. When they arrive at the cave, they discover that Glomgold has built a wall to preventing them from getting in, and the Beagle Boys also abandoned Scrooge's money bin to accompany Glomgold in his plans. The heroes return to the plane to ponder their next course of action when suddenly, the ground gives way underneath causing them (and the plane) to fall underground. Trapped in the cavern, they set out on one of the many pathways which leads to Bubba's cave.
Meanwhile, Bubba and Tootsie arrive back in their own time. Bubba is happy at first to be home again, but he soon realizes that he misses "Skooge", so he decides to travel back/forward in time to find Scrooge. Unfortunately, Bubba has no knowledge of piloting the Millennium Shortcut and ends up causing a few historical incidents along the way. Fearing he could be lost in time forever and with the bar of bombastium nearly gone, Bubba desperately decides to draw a picture of "Skooge" on the machines clock system. The Millennium Shortcut's computer somehow identifies this and sets its course to find Scrooge.
Back in the present, Scrooge and company find themselves at underground lake. To cross, they decide to use Launchpad as a raft (his jacket is airtight when zipped). As they approach land, they find themselves on the run from a sea monster. The chase leads throughout the caverns on dry land and just as the monster corners the group, Bubba and Tootsie appear, landing the Millennium Shortcut on the monster's tail sending it whimpering off into the caves. After a quick reunion, Bubba leads the group to a lower part of the cave, where there are enough diamonds to pay off Glomgold.
Up above, Glomgold and the Beagles are swimming in diamonds when they hear Scrooge and the others. Glomgold glares down in the hole and orders the Beagles to roll a gigantic boulder into the pit to trap them. Trapped, Scrooge asks for ideas to which Bubba replies with a "boom!" Huey, Dewey, and Louie decide that Bubba's idea of an artificial cannon could in fact work. The boys cleverly use some of the diamonds in the cave to reflect sunlight onto a pool of water below, heating the water into a steam cannon, with a gigantic diamond as the cannonball. As the make shift diamond cannonball comes blasting through the boulder, the cave roof itself is blown away as well. A surprised Glomgold is upset, but mocks Scrooge as the group attempt to climb up the cave to pay Flintheart with a diamond worth $10.3 million. But just as the diamond is placed in the hands of Glomgold, he tells Scrooge that the payment is actually late and he is now keeping the island and the cave.
With Scrooge now losing ownership of Bubba's cave, the Beagle Boys shove the group onto a boat and off to the remote island that Scrooge does own. Glomgold, ecstatic with excitement, tosses the big diamond into a crack in the wall, triggering the steam cannon once more. The cave suddenly erupts and sends all the diamonds flying onto Scrooge's island causing our heroes to take cover underneath the boat, from the raining sparklers. Glomgold throws a hissy fit and the Beagle Boys question their life in crime. Bubba sadly says goodbye to his cave. Scrooge has a replica of Bubba's cave built outside of his mansion. As he says goodnight to Bubba, he soon is startled by the loud "rock n' roll" music blaring from the cave. He then proceeds to tell Duckworth to have the cave moved to the other side of the yard in the morning.
- The original 2-hour movie version did not include the sequence where Bubba makes Mung Ho give back everything he took from the people of Tupei. The sequence with the Duckburg Rose Society was also cut.
- Bombastium originated in the Carl Barks comic story "A Cold Bargain".
- The fossilized dinosaur's name is a pun on Roget's thesaurus. The close-captions mistakenly wrote the name as that.
- Apparently, Ma Beagle got arrested somewhere between "Till Nephews Do Us Part" and this - when Burger mistakes the disguised Bigtime for her, he remarks that "she musta broke outta jail!"
- Among the things Bubba destroys in the park is the statue of Cornelius Coot.
- When he starts rolling downhill before the second commercial break in "Ducks on the Lam", Scrooge remarks, "Missed it by that much." This was Don Adams' catch phrase on Get Smart.
- Glomgold shouts to Bubba, "I'll get you, laddie, and your little dinosaur too!" This is a reference to The Wizard of Oz, where a similar quote was said by the Wicked Witch of the West.
- Many of the kids in the classroom can also be seen in the beginning of the Darkwing Duck episode "Toys Czar Us".
- DuckTales: Volume 3