35 years have passed since Lynn Minmay had brought peace between the Zentradi and the humans in the events of Macross. Nekki Basara is a guitarist and a singer of the band Fire Bomber. Living in a less-developed part of the flying colony City 7 which is looking for a habitable planet, he composes and sings songs in the belief that music holds a greater power. During its flight, an unknown alien race appeared and started laying siege upon City 7. However, its attacks are not conventional -- instead of trying to destroy them, they steal what is known as "spiritia", rendering victims unresponsive and zombie-like. During these battles, Basara always goes out into the middle of the warzone, singing his songs and expecting friend and foe to listen and be moved by his music. (Source: ANN)

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. [Written by MAL Rewrite]

Dreaming of a magical world every night, the young Toramizu Ginta yearns to be able to go there. With only his friend Koyuki believing in his dreams, Ginta remains positive despite the slander he receives from others over his dreams. But his wishes are answered, as one day a large door appears in front of Ginta, summoning him to the land of MAR Heaven. In this land, the weapons known as ARMS exist. While initially Ginta greatly enjoyed the discovery of this magical world, he soon learns of the terrible wars that have once plagued MAR Heaven and the upcoming war that may soon appear.

In the year After Colony 196, one year after the conclusion of the intergalactic civil war, a state of stasis prevails over the Earth and its colonies. Seeing no further use for their Gundam mobile suits, war heroes Duo Maxwell, Heero Yuy, Trowa Barton, and Quatre Raberba Winner decide to destroy these weapons by launching them into the sun's surface. Before the Gundam reach their destination, the universal peace is shattered by the emergence of Mariemaia Khushrenada—the only child of the former tyrannical aristocrat Treize. Mariemaia abducts diplomat Relena Peacecraft and announces plans to launch "Operation Meteor," with the intention of posthumously fulfilling Treize's world domination plot. With the help of former enemy Zechs Marquise and his mobile suit Tallgeese, the heroic pilots must reacquire their mobile suits to wage one final battle against the Khushrenada dynasty, including fighting against their former ally Wufei Chang, now aligning himself with Mariemaia's ambitions. [Written by MAL Rewrite]