The film stars the voices of Hugh Grant, David Tennant, Imelda Staunton, Martin Freeman, Salma Hayek, and Jeremy Piven, and follows a crew of amateur pirates in their attempt to win the Pirate of the Year competition.

In 1837 London, Queen Victoria is told that the Royal Navy dominates the ocean, aside from pirates, whom she despises.

After several failed attempts to raid mundane ships, they come across HMS Beagle and capture its sole occupant, Charles Darwin.

Recognizing the crew's pet "parrot", Polly, as the last dodo bird alive, Darwin recommends that they enter her in the Scientist of the Year competition at the Royal Society of London, and the Captain agrees.

Allowing the Captain and his crew to stay at his house for the night, Darwin tries to steal Polly for himself with the help of his trained chimpanzee, Mr. Bobo, but their plan fails.

The next day, the pirates enter the competition while disguised as scientists, and the dodo display wins the top prize, which turns out to be a meeting with Queen Victoria.

The Queen requests that Polly be put in her petting zoo, but the Captain refuses and accidentally reveals his true identity.

The Captain is stripped of his treasure and pirate attire and reveals to his crew that he sold Polly to the Queen, causing them to turn on him.

Back in London, the Captain reunites with Darwin, who has discovered that the Queen is part of a clandestine society of world leaders who dine on endangered creatures and Polly is to be the main course at their next banquet.

The Captain and Darwin steal an airship and locate the Queen's flagship, the QV1, while Mr. Bobo retrieves the crew.

Darwin stays on an island to study more exotic creatures, while the Pirate Captain continues his adventures with his crew, now accompanied by Mr. Bobo.

[20] Hugh Grant, the voice of the Pirate Captain, said that the studio "didn't think the Americans would like the longer title".

He quoted science writer Jennifer Ouellette's 2010 statement at the Science & Entertainment Exchange that scientists are undesirable in American popular culture, being represented as "the mad scientist or the dweeby nerd that dress funny, have no social skills, play video games, long for unattainable women".

[24] Lepra Health in Action and some officials from the World Health Organization claimed that the joke depicted leprosy in a derogatory manner, and it "reinforces the misconceptions which lead to stigma and discrimination that prevents people from coming forward for treatment".

The last thing anyone intended was to offend anyone..." LHA responded that it was "genuinely delighted that Aardman has decided to amend the film", while the trailer was expected to be pulled down from websites,[26] and the final version of the film has "leper boat" replaced with "plague boat".

[30] The film also includes a number of previously released songs by various artists, including "Swords of a Thousand Men" by Tenpole Tudor, "Ranking Full-Stop" by The Beat, "Fiesta" by The Pogues, "London Calling" by The Clash, "You Can Get It If You Really Want" by Jimmy Cliff, "Alright" by Supergrass, and "I'm Not Crying" by Flight of the Conchords.

[40] By August 2011, Aardman had been already working on a sequel idea [48] and by June 2012, a story had been prepared, awaiting Sony’s backing of the project.