Taking place in the fictional Nowhere Islands an unknown length of time after the events of "Mother 2", "Mother 3" story is told in eight chapters, including a prologue. The game begins with twins Lucas and Claus and their mother Hinawa visiting her father, who lives in the northern reaches of the Islands. During their stay, their residence, Tazmily Village, is invaded by mysterious forces known as the Pigmask Army. Hinawa's husband, Flint, is awoken by the Pigmasks' forest fire; upon learning his family has not returned, he searches for them, and discovers that Hinawa has been killed by the normally docile Dragos while protecting Lucas and Claus. As Hinawa is laid to rest, Claus disappears; Flint attempts to find him but is unable to.