The movie is a condensed version of the events in the first Macross series, with new animation. The storyline of the movie does not fit directly into the Macross chronology, and was originally an alternate-universe retelling of the story, but was later retconned as part of the Macross universe. Within the Macross universe, however, it is a popular movie (ie. a movie within a television series), a fact shown in Macross 7. In Macross tradition, it features transforming mecha, pop music, and a love triangle. The movie gets its name from its romantic themes and also by the song sung during its climatic battle sequence by Lynn Minmay (voiced by Mari Iijima). In Macross Frontier, in its first episodes used re-animated famous scenes from the Super Diensional Fortress Macross: Do you Remember Love? and Macross Flashback 2012 to give the viewers glimpes of past events.
Macross's VF-1 Valkyrie variable fighter squadrons attempt to intercept yet another of a series Zentradi attacks on the warship. The Zentradi attack on the UN Spacey consists of Battle Pods (walkers), Fighters, and Zentradi in powered armor. While attacking forces distract fighters, a Zentradi fighter's Warship and its small squadrons attempt to capture the ship itself. The ship's defence forces, consisting of various mecha (a compliment of destroids and other variable fighters) and ship's own weapons attempt to fight off the attack to little effect.
A Small Gunship, with its mini-reflex gun, manages to breach the hull of the Macross, allowing some powered armor troops to penentrate the interior for the ship. Hikaru Ichijyo, a member of the Skull Squadron, disobeys orders to leave the boarders to the ship's internal defense forces, instead following them inside to eliminate them himself.
The large city that resides inside of the ship, which was populated by survivors of island where the Macross was salvaged and rebuilt, had been evacuated to shelters except for two. Pop-singer Lynn Minmay and her manager-brother Lynn Kaifun (known as her cousin Lynn Kyle in Robotech) were trying to get to a shelter near the concert hall she had been performing at when the attack occurred. However, they are cut off from one another when the Macross undergoes Modular Transformation to use its primary weapon, the Main cannon.
Zentradi powered armor inside the Macross spot the two prior to the transformation and Minmay is almost captured by the pair but Hikaru arrives in time to foil the attempt. The Macross then fires its Main Cannon which destroys the enemy warship, causing its fighter forces to flee.
However, the Macross's gravity system had been damaged in the attack which causes it to fail immediately after the destruction of the Zentradi invaders. Minmay is pulled away with the city's debris toward the engine section as ship begins to use its thrusters. Hikaru manages to catch her but crashes into the one the engine area's unmanned compartments.
Here, Minmay and Hikaru are temporarily trapped for few days where they get know one another and begin a relationship. It is during this time that Hikaru explains to Minmay that ship had not heard from Earth since an attack a few months ago. They are rescued soon after and their relationship continues, the two later secretly going on a date which includes taking an unarmed Valkyrie out on a scenic trip as the Macross was making its way near the rings of Saturn. The date is interrupted by the arrival of Misa Hayase and Lynn Kaifun who had pursued them in a shuttle to bring them back.
The four are soon ambushed by Zentradi force that arrive and capture them. Roy Focker arrives (albeit intoxicated) to try stop the kidnapping but fails and is captured himself.
The humans are brought before Vrlitwhai for interrogation which becomes the first contact for the humans, who are referred to as Miclones (as reference to being smaller or microsopic compared to themselves). The Zentradi are confused as to why males and females do not fight one another and why they live together. The captives try explain that this this way they are; that they are born and not manufactured small. They also try to explain that males and females are required to reproduce. The Zentradi force them to demonstrate the reproduction process to them, threating to harm them if they do not. In haste, Lynn Kaifun kisses Minmay which deeply shocks the Zentradi.
The humans later realize that Zentradi males and females do not get along and had been fighting each other with huge armies. As the Zentradi separate the Lynns from Focker, Hikaru and Misa, a female (Meltlandi) force arrives and attacks the flagship. Focker, Hikaru and Misa are able to escape their confinement retrieve their Valkyries and attempt to rescue Minmay and her brother. However, Focker is killed as they try to rescue Minmay and damage to flagship causes Hikaru's fighter be sucked out a hull breach. However, he and Misa fly back, ripping hull plating to try to reach the container which had Minmay and her brother.
Just as they are about to grab them, the flagship initiates a Fold and Hikaru and Misa are flung away from the ship it jumps. However, the pair are caught in the hyperspace bubble of the ship and are briefly dragged through hyperspace, arriving in the skies of a desolate planet.
Alone and isolated, Hikaru and Misa make landfall to try and figure out where they have been transported to. A bare and uninhabited landscape is all they see except they see what appears to be a sea. There, they find remains of the aircraft carrier Prometheus which belonged to the UN Pacific Fleet. It is this grim discovery that tells them they are on Earth.
The pair travels to ruins of Tokyo and finds no signs of life. Radiation from the attack Earth received had apparently disappated long before their arrival making food that they found "safe" enough to eat.
Further out in the ocean, they discover what appears to be a strange tower breaching the surface. They enter the tower and discover that it had been part of a alien city ship. A barely functional computer they access tells them the ship belonged to alien culture named Protoculture and identified Hikaru and Misa as Miclones. It then proceeds to tell them that it was going raise the city with what power it had left. Misa also manages to send a message to Macross of their whereabouts before the terminal dies, the city ship rising out of the ocean moments later.
For few days, the pair explore the alien city, which to their surprise, was designed for human-sized people. Misa also discovers a metal plate which contained an inscription which she is unable to read. After few days of the pair trying sort their feelings of Earth's annihilation and the possibility that they would be alone for rest their lives, they fall in love. It is on that day that the Macross arrives over the alien city.
Upon returning to Macross, Misa and Hikaru report their findings of Earth and the alien city to Captain Global as well as the demise of Roy Focker to Claudia LaSalle. Unfortunately, a Meltlandi scout ship arrives and attacks the Macross. The fight starts off badly for the humans as the the ship uses its main gun, disintegrating the Macross's own main gun and knocking it down onto the city.
Hikaru leads the Skull Squadron against the enemy powered armor squadrons during which Hayao Kakizaki (Ben Dixon in Robotech) is shot down and killed. During this battle, Maximilian Jenius boards the enemy ship in pursuit of a red power armor and the two fight within the confines of the ship's corridor.
As the Meltlandi began to gain an advantage, they halt upon hearing humming/music which is revealed to be Lynn Minmay along with Boddole Zer in his massive flagship. Max defeats the Meltlandi pilot as the Meltlandi ship folds to escape, which is revealed to be Milia, the two falling in love as they hear Minmay's singing.
It is then revealed that the Zentradi saved the Macross as they wished to form a treaty with the humans.
Boddole Zer explains that he is convinced that Human/Miclones had the key to solving the mystery of the Protoculture. The Protoculture were the creators whom allegedly created both Zentradi and Meltlandi as well as the Human/Miclone race. The Protoculture were a dying species which lead them to create their artificial 'children'. They first created the Zentradi and Meltlandi but when they separated the two they began to fight, forming the armies which would wreck havoc across the galaxy for millions of years. The Protoculture then decided to try one more time to create children to carry on after they had gone, resulting in the Human race on Earth. The creators then gave orders to not interfere with the affairs of Miclones.
Boddole Zer had hoped the Humans could use their own culture to solve his problem with the Meltlandi and defeat them using a Protoculture artifact which he had found long ago. The artifact was, in fact, the musical notes on metal plate which Minmay had hummed. Soon after the treaty is signed, the humans' poets try to add words to the song to use it against the Meltlandi army.
Meanwhile, Misa discovers the metal plate she found was, in fact, the words to the song which Boddole Zer had. She translates the words and blend them into a singable human song.
The Meltlandi Main Fleet soon arrives above Earth and Boddole Zer, no longer having any patience to wait for the humans to solve the mystery, orders his fleet try destroy the Macross so the Meltlandi would not get their hands on its secrets, in the process destroying the Protoculture City-Ship. They fail to hit the Macross as it had taken off moments before the attack.
Boddole Zer fires his massive flagship's main gun which destroys the Meltlandi's flagship along with Lap Lamiz. The battle in space is a chaotic three-way between Zentradi and Meltlandi with the humans trying to stay out of the way. During this fight, Minmay comes to Hikaru in his room and tells him she loves him. Misa arrives to tell Hikaru of her discovery and finds the two together. However, Hikaru reaffirms his feelings are for Misa only which leaves Minmay visibly upset as she runs out of the room.
Misa Hayase explains her plan to use the song she translated to stop the fighting to which Captain Global agrees. Hikaru searches for Minmay to try to convince her to sing. She initially rejects it as it was written by another woman but she finally relents and agrees to sing this song, not for herself, but for the sake of everyone.
Macross deploys all its forces as Global has determined flagship must somehow be destroyed if they are to survive the battle. Minemay sings and the emotional effect accrues to both Meltlandi and Zentradi. Vrlitwhai Kridanik, believing he remembers hearing this song from a long time ago, announces he and allies will fight Boddole Zer. Both Meltlandi and Zentradi fleets then turn their firepower onto Boddole Zer's flagship in an attempt breach its hull. It is Vrlitwhai's ship's main gun that finally breaches the hull of the massive flagship.
It is through this breach where the Macross enters the massive flagship, wrecking havoc inside as it fires its remaining weapons to destroy the enemy's ship interior. Hikaru launches his Valkyrie further into the interior of the flagship and finds Boddole Zer whose body is fused with the flagship itself in an organic/cybernetic command center. Hikaru then uses his Valkyrie's entire aresnal and kills Boddole Zer. Zer's death's causes the massive starship to collapse onto itself leaving the Macross and its allies ships intact, ending what would come to be called Space War I.
Hikaru radios Misa and tells her that the mission is accomplished and that he is coming home.
Claudia then asks Misa what was nature of that song to which she replies 'A simple love song.'