Ness was awoken by a Meteor & went out to investigate. As He looks at it,An Insect named Buzz Buzz emerge from it. He warns Ness of an evil being named Giygas. Ness embarks on a journey to seek out & records the melodies from eight sanctuaries.
Ness met Paula,Jeff,& Poo and they journey together. Pokey Minch,who has been seeing Ness agreeing with Buzz Buzz,wish that Ness hasn't found it. Giygas appears to ask him to join him,which he accepts. The Group are confronted by the Starmen. Ness manages to to defeat them with his PK Flash.
Later,They are confronted by Pokey Minch on a spider like machine as the invaders arrives. The Starmen attacks the city. Paula & Jeff faces them while Ness & Poo fought with Pokey and defeats him. Ness confronts Giygas & they battle each other. Paula calls out to everyone on earth to pray. As they pray,Giygas becomes weak,allowing Ness to destroy him with his PK Thunder.
Ness & his friends celebrate as heroes as Paula gave Ness a kiss on the cheek.
Mid-Credits: Pokey Minch survives the attack & was approached by the ROBs,who shows him a Hologram of the Ancient Minister,who asked him to join them.
Post-Credits: Master Hand tells Ganondorf that there's "another boy with PK Powers".