“A glum ho-ho-hum to everyone! I'll put an end to those peppy Brendam-villers' horrific happiness once and for all! There won't be any foolish pranks! Uh-uh! No fun things! Uh-uh! No silly things! I think not! If Professor Otto Wolfgang Zündapp can't have much fun, then neither can that little Kylee pipsqueak! To the Galaxy of Gloom! Here is a new event Zundapp-Mamageddon!”
—Otto planning to literally suck the fun out of Brendam forever and planning Zundapp-Mamageddon.
In the beginning of the film, Snatcher tells Lord Portley-Rind that the Boxtrolls have taken a human baby and vows that he will "protect" Cheesebridge by destroying them in exchange for a White Hat. As the days pass, he warns the villagers of the Boxtrolls, setting a curfew on the town and trapping every troll he comes across with the aid of his henchmen, Mr. Gristle, Mr. Trout and Mr. Pickles.
Zündapp was first seen in an oil rig where he and his fellow Lemons murdered a British agent named Leland Turbo by having him crushed into a cube, much to the shock of Leland's friend Finn McMissile. Upon spotting McMissile, Zündapp orders his gang to kill him, but McMissile escapes and fakes his death.
Portley-Rind's precocious daughter named Winnie notices the trolls and sneaks out of the house. That is when she comes across our hero, Eggs. Unfortunately, Eggs runs off, and Snatcher discovers Winnie and escorts her home. Afterwards, Snatcher and his thugs capture the Boxtrolls including Eggs' adoptive father, Fish.
Determined to save Fish, Eggs disguises himself as a man and sneaks into the village, where he comes across a fairground where Snatcher disguises himself as a performer named Madame Frou Frou and sings the story of the Trubshaw baby's "kidnapping and murder" by the Boxtrolls. After another meeting with Winnie, Eggs slips into Snatcher's hideout, a factory.
Snatcher tests a piece of cheese by devouring it, and his allergic reaction begins, causing his face and hand to swell and begins to hallucinate. Mr. Gristle tosses a bucket of leeches onto his boss, curing him. As Snatcher's henchmen tend to him, Eggs manages to free Fish. The Red Hats discover Eggs and try to shoot him down, but Winnie interferes and Snatcher takes her captive. Eggs swings down on a rope and saves the girl. Both of them run out of the factory and out of the reach of Mr. Gristle.
When Winnie asks Eggs where he came from, Fish tells her that his father, Herbert Trubshaw, was once a famous inventor who cared for the Boxtrolls. When he was a baby, Snatcher ordered the boy's father to build something to help him with his plan. Trubshaw refused and he tried to take the infant from him. The inventor gave baby Eggs to the Boxtrolls for safekeeping and Snatcher supposedly killed Trubshaw by striking him with a wrench.
Eggs and Winnie go to a ball hosted by Portley-Rind. Snatcher, in his Madame Frou Frou costume, nabs him and prepares to throttle Eggs until Frou Frou is called to the dance floor, giving Eggs time to escape. As Winnie teaches Eggs to dance, Snatcher tries to grab him, with little luck. Portley-Rind reveals a giant cheese wheel known as the "Briehemoth" and when Eggs tries to convince him that Snatcher was lying, he accidentally knocks the giant cheese into the river. Portley-Rind tells Eggs to leave his house after our hero tries to expose the exterminator as a fake.
Later, as Eggs (out of humiliation) tells the Boxtrolls that he is not one of them. Suddenly, Snatcher (manning a giant robot) breaks into their home and begins destroying it. As the Boxtrolls first and only instinct is to hide they do the sort and Eggs urges them to get up and fight as Snatcher's machine would kill them however to no avail. Eggs tries to get them to the surface but the machine destroys the way out, Snatcher begins stealing the Boxtrolls and Eggs manages to grab Fish. He has backed into a corner by Snatcher and his goons, he tries to plead but Snatcher mocks him as Boxtrolls lost ten years ago, he orders Mister Gristle to fire, Eggs is tied up then catapulted to a rock wall and is knocked out on impact. Trout and Pickles untie Eggs then Gristle knocks out Fish who was trying to scare them off, they captures Eggs and the trolls and leave.
Inside the factory, Eggs is locked in a cage and notices a crazy man hanging from chains. He realizes that the prisoner is his long-lost father and Snatcher crushes the Boxtrolls in a giant machine before vowing to kill the last one. As it turns out, Zündapp is plotting to sabotage the World Grand Prix, as he is willing to do whatever it takes to eliminate all obstacles and keep everything intact. He even got his gang to murder an American agent Red "Torque" Redline after deducing him as McMissile's contact in Tokyo, though Redline averted this by slipping classified information regarding the plot onto Mater before his death, leaving McMissile and his partner Holley Shiftwell to mistake Mater as a secret agent.
Upon realizing that Mater has got the classified info, Zündapp orders his Lemon gang to track down Mater, though the latter tags along with McMissile and Holley while learning more about the Lemon's plot to sabotage the World Grand Prix. During the second race in Porto Cosa, Mater goes undercover for the Lemons' meeting and soon learns of a horrible truth: Zündapp have created electromagnetic pulse weapons designed as Prix cameras that can ignite the alternative fuel Allinol, which may explain why many racers crashed during the first race in Tokyo. And with Allinol suspended, the world will have to resort back using oil, as the Lemons still own the largest oil reserves in the world. Following the sabotage of the second race, Zündapp receives his next order to kill Lightning McQueen (due to the latter's decision to use Allinol in the third race in London), much to Mater's shock.
The next day, Snatcher seizes power over Cheesebridge and tells Lord Portley-Rind that he has exterminated the Boxtrolls and is ready to off the last one. Eggs is bound, gagged, and stuffed into a Boxtroll costume while the Red Hats dangle him above a furnace. Snatcher is about to place Portley-Rind's hat on his head when Winnie stands up to him and convinces Mr. Trout and Mr. Pickles to redeem themselves, which they do. Unfortunately, Mr. Gristle grabs the controls and prepares to finish off Eggs when Trubshaw and the Boxtrolls, who have slipped out of their boxes before being crushed, attack Mr. Gristle, then lower Eggs and untie him. Winnie then reveals the truth about the Boxtrolls being docile creatures and that Snatcher lied to everyone about Trubshaw being killed by the Boxtrolls when he is still alive. Trubshaw then reveals himself to everyone, making them realize that Snatcher has deceived them all those years. Despite his plot being exposed, Snatcher dons his machine in an attempt to get the White Hat to himself, causing havoc around the city.
Eggs, Winnie, and the Boxtrolls make an attempt to bring down the machine while Winnie and some of the trolls distract Snatcher with the White Hat. In a fit of rage, Snatcher tries to finish off Eggs by striking him with his wrench, but Winnie, Trubshaw, and the Boxtrolls (aided by Mr. Pickles and Mr. Trout) sabotage the robot and it falls down on Mr. Gristle, crushing him to his death. Eggs and Snatcher fall onto the Briehemoth, which has been fished from the river. This triggers Snatcher's cheese allergy, and he grows into a monstrous and amorphous blob. He takes Winnie hostage and forces Portley-Rind to give him the White Hat.
Declaring that he has finally won, Snatcher enters the tasting room, where he forces Eggs, Fish, and Portley-Rind to introduce a new brand of cheese that he wants to taste. Winnie manages to wriggle out of Snatcher's grasp by biting him on the hand. Just as Snatcher is about to taste a small piece of the cheese, Eggs tries to convince him to let go of his lust for power, telling Snatcher that getting everything he wants won't change who he is, and that he has the power to make himself into what he wants to be. Snatcher is taken aback by Eggs's words, and appears to consider them, but ultimately the evil exterminator refuses and eats the given sample. At first, Snatcher finds the taste of the cheese to be delicious, but then seconds later, his allergy finally sets off and he immediately explodes to his death in a yellow slimy mess.
Eventually, Zündapp and his gang are able to track down Bernard and Kylee before trapping them all before heading over to London. After having Grem and Acer to tie up Mater and the agents inside Big Bentley to enact the final stage of their plan, Zündapp fires up the EMP beam on McQueen during the race. However, McQueen unexpectedly escapes unscathed, as it turns out that one of McQueen's friends Sarge switched the Allinol with organic fuel to avoid such an incident, just as Mater escapes to warn Mater. Anticipating that the attempts would fail and that Mater would escape, Zündapp implanted a bomb inside Mater's air filter in hopes that he would set it off to kill both McQueen and Mater. However, Mater uses his rocket booster to speed himself and McQueen out of range, much to Zündapp's anger.
Upon being confronted by a freed Holley and McMissile, Zündapp panics and runs off to the harbor to escape with Tony Trihull (a battleship). However, McMissile snags Zündapp with several hooks before killing Tony with several mini-bombs, allowing him to capture Zündapp. After Mater explains the events to McQueen, Zündapp was soon brought before Mater and McQueen. The captured scientist angrily questioned McQueen on why his death ray didn't kill him, something that shocked the racecar. McMissile angrily orders Zündapp to disarm the bomb, but Zündapp reveals that it can only be disarmed with a voice command by the one who activated it and that neither Mater's nor Zündapp's are a match. This was confirmed when Mater tried to deactivate it, only for the timer to start in five minutes, and when Zündapp is forced to deactivate it, it only shortens it. Realizing that Zündapp is of no use, Holley angrily tasers Zündapp before helping the others finish off the other Lemons for good.
While fighting with Zundapp on the Forever Mountain, Bernard tricks Zundapp to redeem himself to stop Zundapp-Mamageddon, but he accidentally presses The Big Red Power Button, gets zapped with electricity, disappears, and fakes his death. However, he unexpectedly declared Zundapp-Mamageddon passing out forever, in which the power button made him reborn as a giant being.
Bernard and Kylee noticed strange bile coming out of Zundapp's mouth. Zundapp unexpectedly vomited on Lovelace and sneaked away. Zundapp tried to ambush Zig Zag, but Bernard yells "STOP!" to him. Zundapp then tossed Bernard to the edge of the cliff. Zundapp had managed to pin down Lovelace with his giant foot, believing that he had crushed the king to death. Fortunately, Loveace came from under his foot, without being injured at all saying, "Pop goes the weasel" and then running off.
As the quartet go into hiding, Zundapp stalked and found them in one of Franco's wardrobes. However, Zig Zag, Lovelace, and Kylee saved him just as Toto, Joe and the Jolly Brothers showed up and subdued Zundapp.
Zundapp ties Bernard, Lovelace, Zig Zag, Toto, and Joe to a cliff to make them be eaten by his Demon minions and cages the Jolly Brothers. Zundapp climbs with Kylee onto the top of an Empire State Building-like mountaintop to brainwash her as his assistant (like Rex Dangervest did to Olivia). Bernard thinks of a plan to save Kylee and stop Zundapp before it's too late. He invents three F8C-5 Helldiver Navy planes for himself, Toto, and Joe.
They fight Zundapp until Lovelace prepares to fire his cannon-gun with gunfire, and Zundapp gazes at Ann for the last time before being shot, dying and falling from the building and into the sea. As Kylee is reunited with Bernard, the Guardians of Brendam, the Jolly Brothers, civilians, policemen, and soldiers gather around Zundapp's corpse drown to the bottom of the sea. Zig Zag makes his way through the crowd, takes one last long look at Zundapp and says, "It wasn't the airplanes. It was Beauty killed the Beast."
Eventually, Mater soon realized that Axlerod is the true mastermind behind the plot and that Allinol was actually gasoline engineered to ignite as part of the plan. An outraged Mater confronted Axlerod by forcing him to deactivate the bomb to confirm his suspicions. With the plot exposed, Zündapp is presumed to be arrested along with Axlerod and the Lemons for conspiracy to commit crime, murder, and embezzlement.
- All of the advertising presents him as the film's main antagonist. At the end of the movie, it is revealed that he works for Rex Dangervest, making him the secondary antagonist.
- Zundapp' character is based off of Captain Hook and Ebenezer Scrooge.
- The way Professor Zundapp climbs up a tower and carries Kylee with him is a reference to the movie King Kong, in which the titular character climbs up to the top of the Empire State Building, carrying Ann with him.