Like Lego Island, there are 'missions' to do, but in this sequel, they should be completed in a linear fashion. The only playable character in this game is Pepper Roni, unlike the previous game, in which multiple characters were available.

After the events of the previous game and Brickster's recapture, Pepper Roni is promised for a new house, on condition that he delivers pizzas around the island. Having delivered enough pizzas to earn his new house, Pepper is told to deliver a pizza to the jail cell at the Police Station. The Brickster uses chilies saved from previous pizzas to form a fiery, hot pizza breath that melts the jail doors to escape, stealing a police helicopter and flying to the Information Center. He steals the Constructopedia, the book containing the blueprints for all buildings on the island, and then scatters its pages through space and time. All of the buildings on Lego Island are deconstructed. Having summoned the 'Brickster-Bots' of Ogel, the Brickster leaves for Ogel Island (an asteroid floating in space that is inhabitated by aliens and Brickster Bots where the Brickster then resides). Pepper then has to hunt down and destroy the Brickster-Bots by throwing pizzas at them. He then begins to locate a few of the pages. With each page returned, a building is re-constructed.

After helping the Infomaniac on Brickster-Bots in the Information Centre, Pepper then ventures through a portal which takes him to Castle Island (it takes him back to medieval times), where the Brickster has deconstructed the bridge; while diving to connect its two halves, he finds the missing brick pieces and is given page by the citizens which the Brickster dropped. He then engages in a joust to get the Bulls' flag back which was to get a page up the Bulls' castle flag hoist, in which is used as a substitute flag. Before getting the page, he has to engage in a cannon battle against one of the Bulls; Cedric the Bull.

Pepper returns home, collects more pages, then after deputised to be authorised in using the police chopper, flies through another portal to Adventure Island, where he meets Johnny Thunder and his colleagues, Miss Pippin Read and Dr. Kilroy (Johnny Thunder is an Indiana Jones like reference character). With them he defends gems from snakes, recover a page from the Mummies' tomb before being chased by a giant boulder (a Raiders of the Lost Ark reference), race to the oasis in a speedster where he catches a giant fish that swallows a page, and fly in a biplane to the jungle area and rescue some dinosaurs, again getting another page, all from the villain named Sam Sinister, but since his real name was not told in this game, Pepper called him "Mr. Hates". He ventures home on a Pterodactyl arranged by Dr. Kilroy for his trip back.

Pepper again returns to Lego Island, however, Papa & Mama are taken away by the Brickster where they will apparently become his personal chefs on Ogel Island. Pepper then collects the final pages and gets a radio that destroys the new Brickster-Bots, as pizzas don't harm them anymore. After taking out several bots, the Informaniac directs him to go to the space port. All the pages are now supposedly returned.

Pepper then makes his way to the space port, and, after both centrifuge & parachute training, takes a rocket to Ogel Island. Since the Brickster stole the landing gear on the spaceship, Pepper is forced to parachute down to the surface, the training being paid off. On the asteroid, he makes pizzas to send the citizens to sleep, while getting Mama & Papa out of their predicament. He then confronts the Brickster in his Lego palace. In the end the Brickster is left trapped in his palace cage and Lego Island is safe again.

In the final scene, Pepper, Mama and Papa fly home. When they return, one of Pepper's friends (a female one) tackles him and madly kisses him. Soon there is a dance party where everyone is present, later which Brickster-Bots jump out of some crates holding them. However with the music they start dancing, too.

The game has a variety of Lego characters. Many of the characters from the original game, characters like the Infomaniac, Laura, Nick, Papa, Mama, Nubby, and many more familiar faces return. Additional characters are added, people like Darren (one of the producers of the game), soccer players, DJ, Technician Bob, etc. The Brickster Bots were popular enough to be in Lego Soccer Mania in 2002, some of the soccer players even come to the new game.

There are also non-player characters in the game that are based on the Lego minifigures for popular collections of Lego in 2001: people like Johnny Thunder, Cedric the Bull, and Mr. Hates (Sam Sinister or Baron von Barron).

The Station Master serves as a reference to Lego Loco, in which the station master figure would, on occasion, turn into a superhero.

LEGO Island 2: The Brickster's Revenge received fair scores. On the site GameSpot.com, the PC game received 6.8, the PlayStation version received 6.7, the GBA version received 6.9 and the GBC version received 5.9.

• Lego Island
• Island Xtreme Stunts