After the events of the previous game and the Brickster's recapture, Pepper Roni is promised 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 one last pizza to the jail in which the Brickster lurks. The Brickster then adds additional chilies to the already spicy pizza, letting him use is "patented Brickster dragon breath" to melt the lock of the jail cell. He then escapes by stealing a police helicopter and flying to the Information Center, where he steals the Constructopedia, the book containing the blueprints for all buildings on the island. He then tears pages out of the book, causing all of the buildings on LEGO Island to deconstruct. Having summoned the Brickster-Bots, the Brickster departs for his asteroid island, Ogel Island.

The Infomaniac informs Pepper that he must destroy the Brickster-Bots and track down the missing pages of the Constructopedia. He soon begins to locate a few of the pages. With each page returned, a building is re-constructed.

Pepper then ventures to Castle Island, where the Brickster has deconstructed the bridge; while diving to connect its two halves, he finds the bricks and a page. He then finds that another page is up on the Bull's castle flag pole, as the Lions stole the Bulls's real flag. The Bulls promise to give Pepper the flag, as long as he returns the stolen flag. The Lions agree to give Pepper the flag, as long as he defeated the Bull's Dark Knight in a joust. After defeating the Dark Knight, Pepper receives the Bull's flag from the Lions, to give it to the Bulls. However, before the Bulls give the flag to Pepper, he has to engage in a cannon battle with Cedric the Bull, an ally of the Brickster, as he steals the page, just as the other Bulls are about to give the page to Pepper. After defeating Cedric the Bull, Pepper acquires the page, signalling his time to leave Castle Island.

Pepper then returns home, collects more pages, then flies through a portal to Adventurers Island with a helicopter. Upon landing, he meets Johnny Thunder and Pippin Reed, who agree to help him track down the pages on the island as long as he helps them. After defending the Adventurer's truck from snakes as they drive through the desert, they find Dr. Kilroy at some nearby tombs. Pepper retrieves gems from inside a sphinx, then ventures inside the mummy's tomb to get a Constructopedia page. Pepper then drives a car to the desert oasis, to get another page from a large fish that swallowed it, before meeting up again with the Adventurers. The entire team then flies to the jungle, where they learn that Mr. Hates has taken several dinosaurs captive. Pepper rides a t-rex to Mr. Hates's camp and rescues the dinosaurs with the aid of a hot air balloon, then defeats Mr. Hates and gets a page from him. Pepper then says goodbye to the Adventurers and returns to LEGO Island.

Upon returning home, Papa and Mama Brickolini are kidnapped by the Brickster and a group of his Brickster-Bots. Pepper then collects the final pages of the Constructopedia on LEGO Island and earns a special radio from the Radio Station, which now is the only way to stun the Brickster-Bots, as they became immune to pizza.

Pepper then walks to the space port, and, after centrifuge and parachute training, takes a space shuttle to Ogel Island. Pepper's initial obstacle is an asteroid belt leading to Ogel Island, however, he manages to navigate it without much hassle. Since the Brickster stole the landing gear and deconstructs the landing platform on Ogel Island, Pepper has to parachute down. On the asteroid, he makes pizzas to send the citizens to sleep, while getting Mama and Papa out of their situation. He then confronts the Brickster in his palace, locking him in a jail cell at the top of the tower.

Pepper, Mamma and Papa fly home in a Fish Ship, and land on LEGO Island, where the Infomaniac greets them. Pepper's girlfriend tackles him and kisses him, and the scene then fades to a dance party at the Pizzaria. Suddenly, five Brickster-Bots burst out of nearby crates. The music stops, however, the Brickster-Bots start to dance, and the party resumes. The camera then slowly fades and moves away from the party, concluding the game.