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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]

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. [Written by MAL Rewrite]

Eight years after the events of Macross F, a mysterious phenomenon known as the Var Syndrome is gradually consuming the galaxy. It's up to a new generation of highly capable Valkyrie pilots to deal with this universal menace. And if they didn't have enough on their plate already, the Aerial Knights Valkyrie fighter team from the Kingdom of Wind have come to challenge the Delta Squadron.

The movie recompiles scenes from the Macross Δ television anime with new scenes to tell a different story. (Source: AniDB)