In 1837 London, Admiral Collingwood informs Queen Victoria about the Royal Navy's dominance over the seas while also noting their ongoing struggles with pirates. At the same time, the Pirate Captain enters an annual competition on Blood Island known as the Pirate of the Year. This contest centers around the pirate who can steal the most treasure, making it a fierce battleground for pride and glory. After several unsuccessful attempts at plundering various ships, the Captain, along with his quirky crew, manages to raid the HMS Beagle and capture none other than Charles Darwin.
During this encounter, Darwin spots the crew's unique dodo, named Polly, and mistakenly identifies her as a parrot. He suggests that Polly should be entered into the Scientist of the Year competition held by the Royal Society of London, believing this could lead to financial gain. The Captain, seizing the opportunity, enthusiastically agrees to partake.
As the adventure unfolds, Darwin generously allows the pirates to stay overnight at his residence. However, he secretly plots to capture Polly with the aid of his chimpanzee, Mr. Bobo. Despite the plan's execution, it fails miserably. The following day, the pirate crew disguises themselves as scientists and successfully enters the competition. To their surprise, the dodo's presentation wins, but the prize turns out to be nothing more than an audience with Queen Victoria instead of monetary achievement. In a twist of fate, the Queen desires Polly for her petting zoo. The Captain, unwilling to part with Polly, inadvertently reveals his identity as a pirate.
Faced with impending execution, Darwin, who is infatuated with Victoria, discloses Polly's hiding spot, which only the Captain knows. This revelation leads to the Captain being pardoned, with the order for Darwin to locate Polly. In a humorous turn of events, Charles and Bobo attempt to get the Captain intoxicated at a local tavern for a kidnapping attempt that sees them rushing toward the Tower of London, where the Queen awaits. After dealing with Charles and Bobo by sending them down a trapdoor to a garbage dump, Victoria offers the Captain a treasure worth winning Pirate of the Year in exchange for Polly. With dreams of victory, he accepts and returns to his crew.
During the Pirate of the Year ceremony, the Captain is announced as the winner, but his rival Black Bellamy reveals that due to his pardon, he no longer qualifies as a pirate and hence is ineligible for the honor. Consequently, the Captain's treasure is taken, and he finds himself exiled from Blood Island. When he confesses to his crew that he gave Polly away, they abandon him.
He makes his way back to London, where he finds Darwin and Bobo, who have sadly turned to a life of tramps. In a shocking revelation, Charles informs the Captain that Victoria never intended to keep Polly as a pet but rather planned to serve her as a delicacy at an upcoming banquet for world leaders. Determined to save Polly, the Captain and Darwin steal an airship to track down Victoria's flagship, the QV1, while Bobo embarks on a mission to track down the crew.
Once aboard the QV1, the Captain and Darwin find Polly, only to face Queen Victoria. In a climactic confrontation with her, Bobo and the crew arrive just in time. In a chaotic battle, they accidentally mix a stash of baking soda with vinegar, causing a massive explosion that tears the ship apart. As Victoria attempts to flee with Polly in the airship, the dodo bravely attacks her, giving the Captain a chance to rescue his feathered friend. They manage to escape, but in doing so, a furious Victoria revokes the Captain’s pardon.
In the aftermath of these events, Charles is sent to an island to continue his research on new animal species, while Queen Victoria is left vulnerable to the very animals she captured. Ultimately, Black Bellamy is stripped of his award, and the Captain sets off on further adventures alongside his crew, now accompanied by Bobo, ready for whatever the high seas might throw their way next.
