It has been 35 years since Lin Minmei brought peace between the Zentradi and the humans. Basara and his band "Fire Bomber" are a struggling up and coming group on the Macross 7, an intergalactic colony ship traveling through space looking for a new planet to call home. During its flight, an unknown alien race appeared and started laying siege upon the colony. However, its attacks are not conventional - instead of trying to destroy them, they steal what is known as "spiritia," leaving victims in a catatonic state. Basara, yearning to have his music heard, flies into the battle zone in his Valkyrie to spread the message of music.
As the crew and colonists of Macross 7 fleet deal with the threat of their mysterious new enemy, something return to business as usual. Aside from the constant threat of attack, now Mylene must deal with her mother Millia, who is also the Mayor of the city, and her plans for an arranged marriage for Mylene.
Basara and his band "Fire Bomber" are a struggling up and coming group on the Macross 7, an intergalactic colony ship traveling through space looking for a new planet to call home. During one of their concerts, the colony is attacked by a mysterious enemy with an even more mysterious weapon that leaves its victoms in a catatonic state. Basara, yearning to have his music heard, flies into the battle zone in his Valkerie to spread the message of music.
The band get its first taste of real succes when their song "Planet Dance" makes it to 194 on the top 200 list. Mylene meets famous singer Alice Holiday. The Varauta attack and take Alice's spiritia. The movation behind their attacks begin to be revealed when Gepernich cryptically mentions the "Spiritia Farm Project".
Mylene is casted as the lead in the "Linn Minmei story". Mylene is excited about the opportunity, but Basara is, of course, oblivious to this. Mylene's co-star, Bobby, tries to take advantage of her, but he is stopped when a Varauta soldier breaks into their hotel. With Bobby now in a Spiritia coma, Basara is forced to take over the co-staring role.
While Fire Bomber prepares for their "Sound Force" duties, Sivil for some reason is encased in a bubble hidden in a City 7 park. Gamilin is promoted to Lieutenant and given command of the Diamond squad. He requests being assigned to protecting the Sound Force, but instead is placed under the command of Millia, and charged with protecting the city.
Ray takes Basara's Valkerie to the UN spacy for repair. Akiko tells Mylene about how she and Ray met and about his past as a fighter pilot. Ray is injured in a Varuata attack, but goes against doctor's orders to return Basara's Valkerie.
Mylene is kidnapped by a Varauta while on a date with Gamlin. When Basara and the band find out, they run out to go look for her. Gepernich is finally ready to lauch the Spiritia Farm Project, and sends Gigile to attack City 7.
Fame and battles are starting to take it's toll on Basara. The growing popularity of Fire Bomber starts to become more and more evident in City 7. Dokker, who has recovered from his Spiritia induced coma, has been assigned as the leader of the new, elite Emerald squad.
Sivil starts to attack people inside City 7. However, when she hears Basara's music she begins to walk through the streets, and the presence causes the Zentrati to become violent. Elswhere in City 7, a group of terrorists break into the mayor's office, and take Milia hostage.
Mylene, tired of her parents fighting all the time, plots to get them together one last time.
Basara contemplates removing the missile system on his Valkerie. Ray's friend Akiko buys a song Fire Bomber recorded on a hunch that it will become a hit. Gigil confronts Gepernich as to why they are wasting their time on small skirmishes when they could take the whole fleet in one big attack. Gepernich hints that what they learn from the humans could change everything.
Fire Bomber puts on a concert to celebrate City 7's reunion with Battle 7 and the fleet. The concert is interupted when Sivil attacks and starts stealing spiritia from people in the crowd. Later, Max meets with Ray to discuss form a new squad called the "Sound Force".
City 7 gets trapped in the magnetic pull of a nearby star. Milia, Basara and Gamilin do their best to save the city, but the gravitational pull is too strong. As City 7 teters on the edge of destruction, Gigil and the Varauta attack in a final attempt to capture the city.
Mylene and Ray convince Basara that they should ent er the Super Nova Live show for new bands. Tentions rise between Max and Millia when they, as the two leaders of the fleet, get into an argument about the new threat while being interviewed. Macross 7 is attacked yet again, and much to the dismay of the defence forces, Basara flies into the fray to spread his music.
As the Macross 7 fleet search, City 7 de-folds in orbit of a strange planet. While the Varauta recharge the fold engines to rendezvous with Gepernich's fleet, Millia and Fire Bomber work to figure out a way to retake the city.
Milia works with the others to repair the fold system, and to find a way to reunite with the fleet. The Varauta decide that Basara is a liability to their plans, and plot to have him assassinated.