During Apollo 17's 1972 space exploration mission to the moon, humanity found a strange hypergate that led to Mars. Upon entering the gate, the astronauts discovered an ancient technology known as "Aldnoah," which would soon cause mass migration to the planet, resulting in the creation of the Vers Empire to govern Mars. Descendants of this new civilization grew to resent Earthlings for their bountiful resources. These feelings led to a declaration of war, an event that ended with the hypergate's destruction in what would come to be known as the infamous "Heavens Fall." The effects were catastrophic, causing the obliteration of the Moon and irreparable damage to Earth through multiple meteor impacts, earthquakes, and tsunamis.

Fifteen years later, a ceasefire has established a fragile peace, and Princess Asseylum Vers Allusia arrives on Earth in order to promote lasting friendship between the two races. However, not everyone is satisfied with the abrupt end of the first battle; certain forces have been waiting for such a moment in order to ignite the spark that will lead to a new war. When a group of terrorists attempts to assassinate the young princess, Martian soldiers retaliate by launching an assault, descending from space ready to enslave Earth's inhabitants once and for all.