25 years after the battle at Ambat, the war between the Federation and the Vagans keeps escalating with no end at sight as the Vagans rejected all offers for a peace treaty. Flit, now married and father of two is a commander of the Earth forces determined to win the war and decides that the time has come to his son Asemu to succeed him as the pilot for the Gundam, entrusting him with the AGE Device on his 17th birthday. On an attack on his city, Asemu pilots the Gundam AGE-1 hidden at the family's stable for the first time to repel the Vagan offensive.

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.

For 2000 years, a separate race of humanity has lived on the moon. Known as "the Moonrace," their technology is leaps and bounds beyond those that stayed behind on the Earth's surface. Now seeking to return to their original home, the Moonrace send three teenagers - Loran, Keith, and Fran - down to Earth on a reconnaissance mission to test the viability of its environment.

After spending a year on Earth, Loran has become good friends with Sochie and Kihel, daughters of the prestigious Heim family, and he looks forward to fully integrating into Earth society. But before Loran gets the chance to make his report, the Moonrace launch a surprise attack. Earth's primitive airplanes are no match for the superior power of the Moonrace's mobile suits. However, in the midst of the initial attack, Loran and Sochie uncover a long-forgotten relic: a white mobile suit. As a Moonrace, Loran is quickly able to grasp the basics of piloting it, but by doing so, he inadvertently places himself in the middle of a war.

Over a century has passed since mankind sought an outlet in space for its burgeoning population. It is now Universal Century 0100. A new battle, one forged from the experiences of Hathaway Noa once embroiled in the Neo Zeon calamity caused by Char Aznable. The Minovsky Craft equipped Xi Gundam dances wildly through azure skies…

The year is Universal Century 0133. Ten years have past since the armed resistance of the aristocratic fraction, the Crossbone Vanguard, was subdued. Tobia Aronnax is an exchange student onboard the spaceship Smashion to Jupiter, but during a surprised attack by a group of space pirates who call themselves the Crossbone Vanguard, he finds out that there were actually hidden agendas among those in the Smashion and in Jupiter itself. After being saved by a member of the pirates named Kincaid Nau, he was taken aboard the pirate ship, the Mother Vanguard, and was convinced by its captain, Berah Ronah, to join them. The pirate group's true identity was revealed to be a guerilla group resisting the secret fraction within Jupiter, the Jupiter Empire, which intends to conquer Earth. Now Tobia must pilot one of the three powerful Crossbone Gundam to help this new Crossbone Vanguard in their quest to oppose the Jupiter Empire's plans.