This sequel to the Silent Mobius The Movie 1 continues the timeline of the flashback section of the first movie (Katsumis initial contact with AMP), using some more ideas and persons from the Manga, and being slightly less incompatible to the Silent Mobius series from 1998.

The unit Over The Rainbow succeeds in its debut. Aiming to become like the boy band, more students enroll in Edel Rose. Hiro and the others begin practice for the Prism King Cup, an event that is held once every four years. However, a rival called "Schwarz Rose" appears... Who will become the Prism King, the one who can make girls' hearts throb the most!?

The evil overlord Makuamuge is planning to take over both the game and real worlds, and it is up to the ninja Goemon, his friends, girlfriend, and giant robot to defeat Makuamuge's henchmen and save both worlds.

A 300-year-old book is discovered which chronicles the adventures of the legendary Samurai Troopers… centuries before they happen! But what does this mean? Are the Troopers merely puppets in some cosmic play, acting out parts? Who is this mysterious Suzunagi, a mysterious girl who entices each of the warriors with their hearts’ desire - salvation, new armors, freedom from a life of fighting. Why is she so interested in the troopers and their armors?