The game resolves many matters left unchecked at the end of Original Generation 2.5, such as one of the main antagonist's unfinished plan and the activities of one of the enemy factions.

The second gameplay feature is the inclusion of a Free Battle Mode, where the player is given the freedom of setting their own scenario, placing which allied or enemy characters and mechs on the field in a specific environment.

A relatively small and unknown conglomerate, Wong Heavy Industries, introduces its new mech for the Earth Federation Army, the VTX-001 Bartoll.

However, as this unit is mass-produced, large number of civilians around the world go missing and giant, humanoid machines not of Earth origin appear out of nowhere and attack Asakusa City.

Familiar faces make a return, while some will appear most unexpectedly, as the Earth and its citizens find itself yet in another struggle for freedom and destiny...