Five years after the events of the first adventure, the residents of Bricksburg face a new threat: LEGO DUPLO invaders from outer space, wrecking everything faster than they can rebuild. The battle to defeat the invaders and restore harmony to the LEGO universe takes Emmet, Lucy, Batman and their friends to faraway, unexplored worlds, including a strange galaxy where everything is a musical. As Emmet and the gang undertake a perilous mission to rescue their friends from the bizarre, new adversary, the once optimistic and cheerful community must cope with a desolate and post-apocalyptic environment they have now come to call "Apocalypseburg."

In the midst of chaos, Emmet remains unfailingly optimistic, much to the annoyance of Lucy who prefers a more tough and gritty approach. When his friends are kidnapped by the mysterious space invader, General Sweet Mayhem, Emmet embarks on an intergalactic journey to save them. During his quest, he encounters the enigmatic and rugged adventurer, Rex Dangervest, who agrees to help Emmet and teach him how to be tough. As Emmet travels to the Systar System, he faces internal struggle and must decide whether to adopt a new persona to deal with the dangers of the wider universe or stay true to his innately cheery and optimistic self.