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A cinematic retelling of the events of Super Dimensional Fortress Macross, with an adjusted and more compressed story.
The movie opens with the Super Dimensional Fortress (SDF-1) Macross in
space, fending off attacks from the giant humanoid aliens called the Zentraedi. Unlike the series, little
explanation is given to how the SDF-1 got into space, or what the
situation is that led to them fighting the Zentraedi. Hikaru Ichijou is
already a fighter pilot at this point, serving in Skull Squadron with
Roy Focker. During an attack, he gets separated from his teammates
chasing an enemy fighter into the SDF-1. He encounters Minmei Lynn, a
rising pop-star, and saves her from being killed by the attacking force.
While this leads to a budding romance between the two, it also put him
squarely in cross hairs of his superior officer Misa Hayase, who
reprimands him for his reckless choice to pursue the enemy fighters
inside the ship. Hiakru learns nothing from this reprimand, and even
commandeers a recon Valkyrie fighter jet to use on a date with Minmei.
Misa finds out about this, and deploys in a ship with Roy to retrieve
the wayward pair. Unfortunately, as they are arguing about Hikaru's
insubordination, the Zentraedi attack and capture the entire group.
While being taken to interrogation, the Zentraedi are attacked by a
third faction, the Meltrandi. The human group attempts an escape in the
chaos, but Roy is killed in the process, and only Misa and Hikaru are
able to escape. The Zentraedi ship space folds away with Minmei still
prisoner, and causes the Valkyrie Hikaru is flying to get tossed off
course. He manages to land the ship on a barren unrecognizable planet.
At first Misa and Hikaru can't figure out where they could possibly be,
but the discovery of a destroyed UN battleship leads them to realize
they are actually on a devastated Earth. Some how the Zentraedi had
found Earth and decimated it. They travel around the area looking for
survivors, but find none. As the horror sets in, emotions start to run
high and lead to a confrontation between Hikaru and Misa as she
continues to try and pull rank on him, something he finds absurd given
the situation. After yelling at her, Misa finally breaks down leaving
Hikaru shocked as this is the first time he has seen his commanding
officer ever show any kind of weakness. He begins to treat her more
kindly, and attempts to keep her spirits up as they scavenge for
supplies in the wasteland.
While flying in search of supplies, they find what seems to be an alien
tower at sea. Entering the tower, Misa is able to decipher the alien
technology, and initiates an automated program that explains that the
Zentraedi and Meltrandi are connected to Earth's ancient ancestors. As
the ancient race became more warlike, they started to lose their culture (The Protoculture), and divided into two factions: The male Zentraedi and the female Maltrandi. The war between the two has been going on for centuries, neither side remembering the reason for it. After the explanation, the automated systems then reveals the tower they are in is actually part of a larger submerged city, and then proceeds to raise the city out of the water. Amazed by the many revelations they have just listened to, Misa and Hikaru proceed to wander the city in search of more information. Misa stumbles upon what looks like a domestic housing. She finds a small plate among the various items in the house, with writing she can barely translate. She decides to start tiding up the home, and when Hikaru finds her, she has already prepared the dinner table, although there is only water to be served. She begins to express her sadness again, but Hikaru comforts her and then proceeds to kiss her which she does not resist. Sometime later the SDF-1 arrives to rescue them, much to their surprise and joy.
Hikaru is given command of Skull Squadron, and immediately has to fend off an attack from the Meltrandi who have also come to investigate the ancient city. The fight goes extremely poorly, with one of his squad-mates killed and his fellow ace pilot, Maximillian Jenius trapped inside an enemy ship. The SDF-1 is severely damaged in the attack, and just as it seems the Meltrandi are about to finish them off, the Zentraedi arrive and shockingly proceed to save the humans. Even more shocking, they are using Minmei's singing as a weapon to confuse the Meltrandi and force them to retreat. At a press conference, the Zentraedi reveal that they would like to make a peace treaty with the humans, to better understand the Protoculture they had lost all those years ago, such as singing. They return Minmei to the SDF-1, and she immediately runs to Hikaru who is on stage with Misa at the press conference. Instead of being happy to see her, Hikaru looks confusingly at Misa, who can only look at him equally confused. Minmei realizes they both have deep feelings for each other, much to her dismay.
Later, Misa makes a breakthrough in her quarters with the plate she found in the ancient city. Through her careful translation, she discovers the writing is actually lyrics to a song from the ancient Protoculture. She goes to Hikaru's room to inform him of her breakthrough, and discovers that Minmei had already come over to try and win him back. When Hikaru doesn't immediately respond to either of them, Minmei runs from the room in tears. He begins to chase after her, when he hears an equally distraught Misa telling him to go after Minmei. Misa assumes Hikaru would choose the more glamorous Minmei, and that the relationship they had shared in the ancient city was simply situational. Hikaru tells her she is wrong, and that she is the one he wants, not Minmei. Just as they embrace, the ship alert goes off, a massive Meltrandi fleet appears above the Earth, and begins attacking the Zentraedi fleet. The SDF-1's commanding officer, Captain Global, realizes that the Zentraedi peace treaty was only a ploy to help them weaponize the Protoculture for use in the war against the Meltrandi. He orders his ship to immediately take off and launches a desperate last ditch attack against both forces.
Hikaru chases after Minmei, after Misa tells him that she needs to be the one to sing the ancient song to fight the alien forces. The heartbroken Minmei initially refuses, but when she she sees the destruction around her, she realizes she is being petty and childish. She agrees to sing the song, hoping it can save the last of humanity and bring peace. Hikaru jumps into his fighter to join the battle just as the Minmei begins singing. As the song is broadcast to all sides, warriors of both the Meltrandi and Zentraedi factions begin to stop fighting as the ancient song awakens forgotten memories and feelings in them. Not happy with this outcome, the Zentraedi fleet commander begins to use his massive mothership to attack all those around him, hopping to annihilate everyone and finally win his endless war. A quick alliance of Humans, Zentreadi and Meltrandi launch an assault on the mothership, with the SDF-1 in lead. The SDF-1 rams through the exterior of the giant mothership, with Hikaru providing close air support. As they get inside, Hikaru goes solo again, this time saluting with his mech to Misa, before flying off into the heart of the ship. He finds the Zentraedi commander at it's core, merged with the mothership in a mess of bio-organic wires. Defenseless, Hikaru easily kills the insane Zentraedi leader with his Valkyrie fighter and ends the conflict. As the crew on the bridge of the SDF-1 relaxes, one of Misa's fellow officers asks her what kind of song it was that had been able to so drastically turn the tide of battle. Misa replies: A simple love song. The film ends with Minmei quietly tapping her feet in time, just before bursting into song as the credits begin to roll.