The game immediately casts the players as Pepper Roni, the pizza delivery boy of Lego Island. The Infomaniac informs him that the people of Lego Island are donating bricks to build his new house for him, but first, he must deliver pizzas to them. When Pepper delivers the pizzas and has his house built, Papa Brickolini calls him for one last pizza delivery job. Pepper must deliver a pizza to the Brickster in jail. Upon arrival, Pepper learns the Brickster has been saving peppers from the previous pizzas, so he can eat them all at once and melt the jail bars with his fiery breath.
The Brickster then steals the police helicopter and the Constructopedia, the book with all instructions to the buildings on Lego Island. With each page he tears from the book, a building becomes deconstructed and the pieces fly into the air. The main plot of the game starts here, where Pepper must travel three different worlds to collect all the pages and rebuild Lego Island. The Brickster releases his "Brickster Bots," robotic minions that taunt and terrorize the people of Lego Island. Pepper uses pizzas to break them down. For every Constructopedia page Pepper finds, a building is restored. After finding four pages on the Island and dealing with the Brickster Bots in the Information Center, Pepper must travel to Castle Island by boat.
On Castle Island, Pepper must rebuild the bridge between the Lions and the Bulls, two kingdoms on separate halves of the island. Pepper dives down the river and avoids obstacles such as sharks, firing cannons, a giant squid, and skeleton pirates. He rebuilds the bridges and collects a Constructopedia page. After that, Pepper must joust the Dark Knight in order to get the Bulls' flag from the Lions. The stubborn Bull leader, Cedric the Bull, is adamant about giving Pepper the page. Pepper must blow up all the Bulls' cannons using his own, while also dodging cannonballs from Cedric. Upon his defeat, Cedric surrenders the page and the Castle Island stage of the game is complete.
Several more pages are found on Lego Island after returning. Pepper also collects a boombox used to defeat the Brickster Bots (since pizzas no longer hurt them). Shortly thereafter, Pepper is told he must go to Adventurers' Island via helicopter. He lands in the desert and meets classic Lego characters Johnny Thunder and Pippin Reed. On their way to the Sphinx, Pepper must prevent snakes from stealing the Adventurers' gems by using a cannon in the back of the Scorpion Tracker. At the Sphinx, they meet Dr. Kilroy, who agrees to let Pepper use his Speedster to get to the Oasis. Pepper must open sarcophagi to match symbols and open the gate to obtain a page. A boulder is triggered and rolls towards Pepper towards the exit. Pepper then gets into Dr. Kilroy's Speedster and avoids rocks, trees, cows, tornadoes, and UFOs on the way to the Oasis. At the Oasis, Pepper fishes for a fish called Big Bertha, who swallowed one of the pages. At the airfield, Dr. Kilroy has succumbed to heat exposure. Pepper must fly the biplane to the jungle, while the three Adventurers fly in the seaplane.
In the jungle, Pepper rides a T-Rex to the infamous Mr. Hates' camp. Mr. Hates has a page. Pepper frees all of Mr. Hates' dinosaurs that he has captured and retrieves a page. The Adventurers Island part of the game is complete, and all of the pages have been returned to the Island.
Upon returning to Lego Island, Pepper begins training to go into Space, as reports indicate the Brickster has settled on Planet Ogel – "Lego" spelled backwards. Pepper trains for centrifugal force and parachute emergency. During space travel, Pepper dodges asteroids and finds that the Brickster has stolen the landing gear. He must jump out of the shuttle and parachute onto Ogel Island.
On Ogel, Pepper makes pizzas with Mama and Papa Brickolini, whom the Brickster has taken captive. The pizzas put the citizens of Ogel to sleep so Pepper can face the Brickster. He climbs the tower, avoiding moving platforms and gaps. At the top of his tower, Pepper must throw spicy pizzas at the Brickster whilst dodging Brickster Bots. When the Brickster eats three pizzas, he goes to the bathroom sink for water and locks himself in, effectively jailing him again. Pepper and the Brickolinis return to Lego Island.
While the game is mostly made up of mini-games, the player can explore each Island in-depth to retrieve trinkets scattered around the map to boost their score. Castle Island has chalices, Adventurers Island has red gems, and Ogel Island has yellow crystals.