In 1837
London,
Admiral Cuthbert Collingwood tells
Queen Victoria that the
Royal Navy has defeated
France,
Russia,
Portugal,
China and
Wales. She assumes that the Navy now dominates the world's oceans, but Collingwood tells her that they are currently dealing with pirates, whom she detests and demands to have them disposed of. The Pirate Captain, who leads a quirky crew of amateur pirates, enters the annual Pirate of the Year competition held on Blood Island, the home of all pirates, where the winner is determined by who can steal the most treasure. After several attempts to raid ships that do not have any treasure, they raid
HMS Beagle and capture
Charles Darwin. Recognizing the crew's
dodo, Polly, who they believe is a
parrot, as
the last of her species, Charles recommends that they enter her in the Scientist of the Year competition at the
Royal Society of London. Thinking that the prize is
money, the Captain agrees. Allowing the pirates to stay at his house for the night, Charles tries to kidnap Polly with the help of his
chimpanzee, Mr. Bobo, but fails. The next day, the pirates enter the competition while posing as scientists and the dodo display wins the competition. However, instead of money, the prize turns out to be a tiny trophy, encyclopedias and a meeting with Victoria. She requests that Polly be put in her petting zoo, but the Captain refuses and inadvertently reveals his true identity. When he is about to be
executed, Charles informs Victoria that Polly has been hidden and only the Captain knows where; she
pardons the Captain and orders Charles to find Polly by any means necessary. Charles and Bobo get the Captain intoxicated at a
tavern and attempt to kidnap Polly. The Captain chases them into the
Tower of London, where Victoria awaits. After she sends Charles and Bobo down a
trapdoor into a garbage dump, she offers the Captain enough treasure to win Pirate of the Year in exchange for Polly; he accepts the offer and returns to his crew. At the Pirate of the Year ceremony, he is declared the winner, but his rival, Black Bellamy, reveals Victoria's pardon and explains that as a result of this, he is no longer a pirate. Consequently, he is confiscated of his pirate attire and treasure and
exiled from Blood Island. When he reveals to his crew that he gave Polly away, they abandon him. The Captain tries to make a living knitting and selling baby clothes in London before deciding to rescue Polly. However, he discovers that she is not in at the petting zoo. He reunites with Charles and Bobo, who have become
tramps. Charles reveals that Victoria did not want Polly for the petting zoo and he has discovered what she actually wanted Polly for. After he and Bobo landed in the dump, he learned that she is part of a club of world leaders who dine on
endangered animals aboard her
flagship, the
QV1. Polly is the main course at their next banquet. The Captain and Charles steal an
airship and locate the
QV1, while Bobo goes to look for the crew. Aboard the
QV1, the Pirate Captain and Charles find Polly, but are confronted by Victoria. Bobo and the crew come to their rescue, but while fighting Victoria, they mistakenly combine a stash of
baking soda with
vinegar, causing an explosion that breaks the
QV1 in half. Victoria attempts to escape with Polly in the airship, only for the latter to retaliate, resulting in her being dropped; the Captain catches her and the pirates escape. Charles is taken to an island to continue discovering new animal species, while Victoria becomes in danger of being eaten by the animals that she captured. The Captain is no longer pardoned and declared the most notorious pirate in the world. As a result, he is reinstated as a pirate and his exile on Blood Island is lifted. He continues adventuring with his crew, now accompanied by Bobo. ==Voice cast==