The film unfolds in the year 1837, following the misadventures of the Pirate Captain, an inept yet well-meaning leader of a mismatched crew of amateur pirates, each with their own quirks and idiosyncrasies. Together, they aspire to carve out their own legendary status amidst the perilous expanses of the high seas. To validate his worth and that of his crew, the Pirate Captain decides to enter the prestigious Pirate of the Year competition. This contest rewards the pirate who can plunder the most during the year, presenting a golden opportunity for the underdog captain to make his mark.
However, when our protagonist attempts to submit his entry, he is met with scorn and ridicule by well-established pirate figures—Captain Bellamy, Cutlass, and Pigleg—who overshadow him with their remarkable successes and lavish exploits. Following a series of fruitless efforts to loot commonplace vessels, a disheartened Pirate Captain confides in his loyal first mate, the Pirate with a Scarf, expressing his temptation to abandon piracy altogether and instead delve into the world of selling baby clothes. Fortunately, his comrade persuades him to seize the opportunity to commandeer the next ship they encounter, which ultimately leads them to the illustrious Beagle.
Upon boarding, they do not find treasure; however, they manage to capture the renowned scientist Charles Darwin. In a delightful twist, Darwin observes that the crew's pet parrot, Polly, is the last surviving dodo. He eagerly encourages the Pirate Captain to present Polly at the upcoming Scientist of the Year competition hosted by the Royal Academy in London, promising a substantial reward for the winner. Undeterred by warnings of Queen Victoria's notorious disdain for pirates, the Pirate Captain directs his ship towards London, hoping to secure a new avenue for fame.
Darwin, motivated by a desire to impress Queen Victoria—who he has an infatuation with—solicits the help of Mr. Bobo, his trained chimpanzee, employing cunning tactics to apprehend Polly in order to claim the ultimate glory for himself. Despite witnessing this unscrupulous act, the Pirate with a Scarf manages to alert the ship's crew, yet the chaos of the attempted kidnapping ensues. Tensions rise as Darwin deftly avoids the blame while the Pirate Captain decides to conceal Polly and participate alone in the competition, which frustrates Darwin to no end.
At the much-anticipated award ceremony, the Pirate Captain inadvertently reveals his identity, which puts him in perilous jeopardy. Yet, Darwin ingeniously persuades the Queen to grant the Captain a reprieve, claiming that only he knows Polly's whereabouts. The Queen grants him a full pardon but commands Darwin to retrieve the dodo at all costs. Thus, the two embark on a comical yet dangerous journey, culminating in the revelation that the dodo is cleverly hidden within the Captain's beard.
As events unfold, our Pirate Captain's misadventures lead to chaos aboard the QV1, where Queen Victoria's elaborate dining plans involving rare animals are thwarted. In a raucous showdown, the duo, along with the Pirate Crew, confront the Queen, who explains her disdain for piracy before attempting to take their lives. With lives hanging in the balance, a disastrous mixing of ingredients leads to a catastrophic explosion that splits the ship apart, allowing the Captain to rescue Polly in the nick of time.
Ultimately, having reclaimed his place among pirates, the Captain and his loyal crew set out once more to tackle the thrilling and treacherous waters in search of adventure. They leave Darwin on the Galapagos Islands to pursue his romantic interests, while Mr. Bobo joins the Captain's merry band of misfit pirates. As for Queen Victoria, she watches helplessly as she becomes surrounded by the very rare animals she had intended to feast upon, leaving her at the mercy of her own designs.
