1,000 years have passed since the events depicted in Phantasy Star Online 2. A new generation of ARKS settled on Planet Halpha. For decades, ARKS has been dealing with a new threat known as the DOLLS, creatures whose origin and purpose is unknown. Joining ARKS are also Meteorn, individuals arriving from outer space through pods. Meteorn possess no memory of their life prior to arriving but regardless possess skills that make them effective against the DOLLS and join sides with ARKS to fight against the DOLLS.