The Hakurei-Moriya Conflict. A war that has been ongoing for more than 8 months. The bodies of Human and Youkai alike have been piling up on both sides, but the Principality of Faith has finally brought the Human Federation to its knees, leaving but one last sanctuary -- Colony Hakurei. Ever since the Principality of Faith has launched the G3 gas attack on the Earth by Major Shameimaru Aya on the fateful day of 9/11 in the year 20XX, the death toll on the Federation side has spiked to 11 million, contributing to the total amount of deaths on either side, human or Youkai, to bring about the total of 18 million valiant Man and Woman who have lost their lives in the conflict. Fearing the gas attacks, the humans have been driven to Colony Hakurei. They could not stop the enemy's superior technology -- the standard issue mobile suits of the Principality, Guntanks, had the AWMS (Active Wind Manipulation System) granted to them with their unique FAITH (Further Acceleration Intertia Technology reactor Hans) drives. This allowed the unit to be controlled with extreme precision and reduces air resistance on the mobile suits, allowing for them to outmaneuver the far slower GMs and the comparitively harmless Type 61 Tanks that the Federation have in service. With machines developed by K.A.P.P.A, the Principality is far well armed than the Federation is.

However, unbeknownst to the Principality, a young woman known as Reimu Hakurei came into possession of a machine that was excavated from the BORDER. This unknown machine, carved with the name "GUNDAM" came to be known as UDMS-01 (UnDefined Mobile Suit). Enlisting the help of the Junk Guild lead by Mr Morichika Rinnosuke (Now Lieutanant Morichika Rinnosuke), the GUNDAM was reverse engineered successfully into GUNDAM BORDER, named after its drop site.

Now the test pilot of the BORDER, Hakurei Reimu fights alongside the newly developed SHRINE Class Mobile Fortress, the Positive, armed with the Pyramid Defense System developed by President Kamishirasawa Keine in a last-ditch effort to produce a weapon that could single-handedly win a war. Fighting alongside Commander Alice Margatroid and Ace Pilot "Magician" Major K. Marisa, Hakurei Reimu resolves to avenge the deaths of her parents that died in the Gas attack during their visit to Earth.

It is C.E. 73. The Federation is determined to destroy the Principality Of Faith and execute President Yasaka Kanako.