After warping light-years away from Earth, the spacecraft Macross carries a city of civilians and soldiers back home. They continuously fight off the threat of the Zentradi and Meltrandi, giant alien races with whom humanity wages war. During a battle, the Macross transforms into a mecha operated by fighter pilot Hikaru Ichijou. Thrust into a number of hardships, Hikaru grows close to the city's idol Minmay Lynn. As their relationship develops, however, it is viewed unfavorably by others due to Minmay's status and popularity. With war raging on and the state of Earth unknown, Hikaru and his fellow soldiers fight on against their mysterious enemies. Throughout the bloodshed, Hikaru and Minmay attempt to keep hold of their feelings for one another. Minmay pours her heart into her music, which may just turn out to be the key to finding peace.

All his life, Shiki has been surrounded by machines. At Granbell Kingdom, a long-abandoned amusement park, he is the only one of his kind around. That is, until Rebecca Bluegarden and her feline companion Happy arrive, unaware that they are Granbell's first visitors in one hundred years. Their goal is to make fun videos for their B-Cube channel, but what they find instead is a friend in the socially awkward Shiki. When Granbell becomes too dangerous for the three of them, they set off on an adventure through the Sakura Cosmos. They hope to make more interesting videos and even find the elusive goddess Mother, while Shiki wants to make more friends, spurred on by the words of his late grandfather. Of course, the journey will not be easy, as no one has seen Mother before, but Shiki is determined to reach his goal and explore the boundless reaches of space together with his new friends.

The alien invader Goa plots to conquer the Earth. He first warns the Murakami family (father Atsushi, mother Tomoko, and son Mamoru) of their invasion, and demonstrates his powers by transporting them to a prehistoric jungle and destroying a Giant Dinosaur before their very eyes. But they will not agree to surrender to Goa, so hope comes in the form of Magma, an armored, golden giant with long hair and antennae. He and his human-sized wife Mol, both created by the wizard Earth are sent to defend our world against Goa. They befriend Atsushi and Mamoru, the latter has Magma emotionally touched, as he wanted to have a child with his wife Mol, so Earth creates a duplicate of Mamoru, named Gam Earth gives Mamoru a whistle, with which he can call Gam Mol and Magma in times of crisis. So when Goa unleashes his various daikaiju, chances are, Magma, Mol, and Gam will fly to the rescue.