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.

A.D. 2040—Thirty years have passed since the battle between the Earth and Zentraedi forces changed the lives of both races. On planet Eden, a top-secret project known as Supernova is being held to determine U.N. Spacy's next-generation variable fighter. Competing to win the funding are Shinsei Industries' YF-19 and General Galaxy's YF-21. Piloting the YF-21 is Guld Goa Bowman, a half-human, half-Zentraedi. Shinsei receives its new test pilot in the form of the unruly fighter pilot Isamu Dyson, who was once a friend of Guld. Meanwhile, as Isamu and Guld furiously battle to see which of their fighters is superior, a Virturoid Idol named Sharon Apple is to perform her debut concert on Eden. In charge of Sharon is producer Myung Fang Lone, another former friend of Isamu and Guld. When the three meet each other, old disputes spark from a troubled past. Little do they know that their past incidents—along with the Supernova Project and Sharon Apple—will somehow bring them together. (Source: ANN)

Less than a year after the events that transpired in the Macross 7 TV series, Basara leaves Fire Bomber and travels to the planet Zola. There, he meets a girl named Elma, who is a big fan of Fire Bomber. It is also on this planet where he must once again use his Spiritia powers; this time, to stop an army of poachers and Elma's father Graham from killing a group of space whales travelling within the planetary system.

Following a catastrophic war against a race of giants known as the Zentradi, humanity has escaped towards the center of the galaxy aboard a fleet of colonial vessels called the Macross Frontier. As the extraterrestrial threat is left further and further behind, life on Macross Frontier proceeds as usual. In the year 2059, a young mecha pilot trainee named Alto Saotome and his colleagues are preparing to perform an accompanying routine for the famous singer Sheryl Nome, who has come to Macross Frontier for a concert. During the performance, a biomechanical alien species known as the Vajra make a sudden appearance, breaking through the defensive perimeter surrounding the vessel and crash-landing near the concert venue, plunging the entire city into chaos. As the concertgoers evacuate, a young girl named Ranka Lee is left behind and gets targeted by the Vajra, but she is saved at the last minute by Alto. Following these events, the Strategic Military Services program notes Alto's skill in battle, resulting in his recruitment to combat the new alien threat.