Master Builders are a group of elite builders and creators who were rumored to have made the LEGO universe. Now every so often during the events of the Kragle Incident, the Master Builders meet in Cloud Cuckoo Land, After the destruction of Cloud Cuckoo Land and the end of the Kragle Incident following the Victory at Bricksburg, the Master Builders recreated Cloud Cuckoo Land and eventually turned it into a field Head Quarters during the Lego Clay War, where they used it to store the last of the Lego Universe's resources.
Lord Business was confused by all this, so he stopped all creating by placing borders around the universe and hired Bad Cop/Good Cop to arrest the Master Builders by leading the Super Secret Police. Those who were not arrested either snuck out of Bricksburg, hid out in the tunnels between the different lands, or live amongst the rest of the city incognito. Those who were arrested by the Super Secret Police were locked up in Lord Business' Think Tank to make instruction books.
Some of the Master Builders were captured by Lord Business' forces during MetalBeard's earlier invasion of the Octan Tower.
Later on, the Super Secret Police apprehended most of the remaining Master Builders during their raid of Cloud Cuckoo Land.
After Emmet's sacrifice to stop the Think Tank from delivering a deadly shock to the imprisoned Master Builders, the captive Master Builders were freed and assisted the rest of the minifigures that built different objects in their battle against the Micro Managers. Upon his return, Emmet gained Master Builder abilities which proved instrumental in convincing Lord Business to place the Piece of Resistance on the Kragle. Once that was done, the Micro Managers shut down and President Business distributed the antidote to the Kragle on those who were "Kraglized" while the Master Builder and other minifigures celebrated Emmet's victory.