After surviving a brutal terrorist attack on Plant Quetta, Suletta Mercury returns to dueling at the Asticassia School of Technology, while Miorine Rembran sits at her injured father's side, waiting to see if he will recover. As the residents of Earth House are preoccupied with their respective troubles, two members of Dawn of Fold—the perpetrators of the attack—secretly infiltrate the school, putting Suletta and her friends at risk. At the same time, Prospera, Suletta's mother, approaches Miorine to propose the continuation of Quiet Zero—a project headed by Miorine's father that can allegedly end all war. Prospera seems to be another political figure with hidden, opposing motives, and whether she truly has Suletta's well-being at heart remains to be seen.

Drift peacefully into Neo Venezia, a city on the planet Aqua (formerly known as Mars). By the 24th century, humans have found a way to colonize the previously uninhabitable planet. As futuristic as that sounds, Neo Venezia is still teeming with rustic beauty; gondolas on wide canals and waterways are the main mode of transportation. The city itself is a faithful replication of Manhome's (the planet formerly known as Earth) Venice. To make sure that residents and tourists alike get the most from Neo Venezia's many wonders, companies offering guided tours via gondola were formed, one of which is named Aria Company. This is the workplace of Akari Mizunashi, a free spirited teenager from Manhome who is now a novice Undine (the title given to tour guides). Join Akari as she becomes intimately acquainted with other Undine, tourists, Neo Venezia's residents, and even the city itself, learning many valuable life lessons along the way, such as the wonderful truth that there are such things as manmade miracles.

In the year Universal Century 0096, three years after Char Aznable's failed attempt to force human migration into space, life continues in the colonies orbiting Earth. One such colony, at Side 4, is home to Banagher Links, a 16-year-old who lives a quiet life among his classmates. Audrey Burne, the last descendant of a great tyrannical family, takes it upon herself to steal the key to a mysterious device known as Laplace's Box. It is said that the Box has the power to shape the course of the universe, and Audrey travels to Side 4 in an attempt to take it from its current holder and keep it from the Sleeves, the surviving remnant of Char Aznable's Neo-Zeon. In her search, she stumbles across Banagher and changes his life forever. When Side 4 comes under the attack of the Sleeves and its prolific fighters Marida Cruz and Full Frontal, Banagher takes control of the newly built Gundam Unicorn to defend his friends and protect the fate of humankind.

In Terra Formars Revenge, the crew members of the Annex I continue to fight against Terraformars—the large humanoid cockroaches that evolved from the ones sent to Mars centuries ago. However, far from discovering the cure for the lethal Alien Engine Virus that has been plaguing Earth, the Annex I team have learned that some squadrons have agendas from their own countries. Now, the squadrons must not only fight against the Terraformars for their survival, but also each other in the never-ending battle for international dominance.