The game's overall plot deals with the sudden appearance of a second, war-torn Earth from which new and more deadly enemies emerge.

At the same time, enemies who survived the First Defensive War begin reappearing on the original Earth, further complicating matters.

Both sides abandoned the use of the Baldora Drive 18 years ago, but recently brought it back into service when they obtained the means to repair it.

However, as the wormhole expands due to the effect of the Baldora Charge (which is used to power the device) obtained from various sources of energy, the wormhole grows large enough to make the two earths collide with one another due to gravitational attraction, which will destroy all mankind on both Earths.

), the Ra Cailum and its captain, Bright Noa, also appears in the game, but due to the death of Hirotaka Suzuoki (the voice actor for Bright) in 2006, most of his scenes in the game are cut, and his voiceovers reuse recorded material from A.C.E.