A military test accidentally sends a modern-day army back in time to feudal Japan. When their actions in the past begin to have an effect on the present, another unit is dispatched to retrieve them. But the commander of the lost unit has other plans: He wants to use his advanced technology to conquer Japan and change his country's destiny.
(Source: CMX)

U.C. 0097, one year after the opening of "Laplace's Box." Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered.
The conflict later dubbed the "Laplace Incident" is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten.

However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix... named Phenex.

The year is Universal Century 0096, and Banagher Links is a student at the Anaheim Electronics Industrial College training facility at an incomplete space colony. There, he rescues a girl named Audrey Burne and helps her to evade capture by Zeon remnants known as the Sleeves. The Sleeves are after "Laplace's Box" an item the Vist Foundation has had in its possession since the beginning of the Universal Century which can be used to topple the Earth Federation government, and Cardeas Vist, the head of the family plans to hand them the key to it. Audrey, fearful of what will happen, wants to convince Vist not to give them the key. The Earth Federation's Londo Bell unit attacks the Sleeves and Banagher is drawn into the chaos.

Adapted from the light novel series that were later adapted into a feature film series, the first of which has already been released this February 2010.