Two years have passed after the final battle with Boddole Zer. The Macross is now a relic of the conflict known as Space War I, and sits in a large lake in barren Alaska. Earth is still a desolate wasteland, and small towns and forests are located miles around Macross City. The allied Zentradi fleets, along with the citizens from the Macross, maintain a nervous peace. The work to rebuild Earth by both sides is in full swing. Hikaru looks back on the times spent with Roy Fokker for advice on what do about his feelings for both Misa and Minmay.

A epic battle for the Earth takes place when Boddole Zer's main fleet of over 4,000,000 warships fold above Earth's atmosphere. Using the power of song from Lynn Minmay, the Macross, along with its allied Zentradi fleet, attempts a daring last stand to Boddole Zer's forces. Heroes will die, a world may fall, but will love prevail?

In a surprising turn of events, Exsedol Folmo is micronized and attempts to seek peace negotiations with the people of the Macross. During the negotiations, Exsedol reveals that the defection of the Zentradi soldiers could be related to a new cultural awakening caused by Minmay's songs. Hikaru begins to long for Misa, who is still on Earth, trying to convince her father and the UN that the two races may have a chance of co-existing peacefully.

Max encounters Milia in the park and a knife fight between them ensues when she reveals that she is a Zentradi. Max defeats her for the third time, sparing her life, and the two fall in love. Milia decides to join the Macross and their immediate marriage marks the first union between a human and Zentradi, causing celebrations everywhere along Macross City. Boddole Zer, on the other hand, doesn't like the idea and plans to fix the 'contamination' that is human culture once and for all.

Max has a chance encounter with Milia in a video game arcade, and proceeds to defeating her a second time during a game. They arrange to have a date in the park later, where Milia secretly plans to destroy him. Misa is escorted back to Earth by Hikaru, so that she could meet her father.

The battle within the city comes to a close, with the surviving Zentradi defectors coming to terms with the destruction they caused. Along with Rori, Konda and Warera, the defectors are all given asylum within the Macross. Misa prepares to travel back to Earth to the UN Headquarters, whilst Hikaru begins to further contemplate his feelings for her.

Zentradi soldiers - having experienced and enjoyed some elements of human culture brought back by the three spies - attempt to defect to the Macross. A Daedalus Attack on Britai's ship allows them to pour through. During a concert by Minmay, a confusing three-way battle ensues inside the ship, with Zentradi refugees against Quamzin's forces, and the unwitting UN Spacy on the other side.

Milia is now aboard the Macross as a spy and marvels at human culture. The premiere of Minmay's film Shao Pi Long (Little White Dragon) takes place. A Zentradi attack prompts another transformation to combat mode, and Hikaru and Misa end up being trapped within the walls of the ship, where they end up learning more about each other. Milia continues to search for the miclone pilot who defeated her.

After the catastrophic events in the previous encounter with the Zentradi, the UN orders the Macross to leave Earth in order to give the UN Spacy more time to formulate a defense plan against the aliens. Returning once more to Britai's ship, the macronized Zentradi spies bring back 'samples' of culture to their dumbfounded comrades.

Still feeling the effects of a tragic loss from the previous battle, Hikaru is assigned a new Valkyrie fighter. Global wants to test out a barrier defense system against a new attack by Quazmin. But for the Ontario region where the battle takes place, this could end in disaster. And in the female Zentradi fleet, Milia approaches her commander, Moruk Laplamiz, to gain permission to be micronized so she could infiltrate the Macross.

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A special clip episode where following a severe injury sustained in the previous episode, an incapacitated Hikaru lies in a hospital bed inside the Macross, dreaming about the previous events and his developing relationship with Misa and his ill-fated friendship with Minmay.

The crew of the Macross are informed to not let anyone, including civilians, leave the ship, so as to keep the truth of the Zentradi's existence from causing widespread panic. The civilians within the Macross become increasingly unruly and violent toward the military personnel and crew members. Meanwhile, Quamzin returns, breaking orders and attacking the Macross while it sits in the Atlantic ocean.

Whilst Misa and Global travel to the Alaskan headquarters of the new UN, Hikaru escorts Minmay to Japan so that she could visit her parents. Lynn Kaifun, a relative of Minmay, joins the Macross to see his parents and protect Minmay.

In this clip show, Global recounts the events of the story up to this point.

With Earth only two days away by full speed, Global decides to ram the Macross through a Zentradi blockade. Meanwhile, Rori, Konda and Warera begin to explore human culture up close in micronized form.

As the four miclone prisoners attempt to make their escape, a fearsome female Zentradi pilot, Milia Fallyna, attempts to approach the Macross on her Queadluun-Rau powered armor to help sneak aboard the three Zentradi spies - now micronized to human size.

After being captured by the Zentradi, Misa, Hikaru and Kakizaki are 'interviewed' on human culture by Britai, Exsedol, and Supreme Commander of all Zentradi forces, Golg Boddole Zer - marking the first verbal encounter between the two races. They discover that the Zentradi have no sense of culture and fear intimacy between men and women. Max, having been separated from the others, formulates a plan to rescue them. Meanwhile, Minmay begins a singing career on the Macross.

Rori, Konda and Warera - three Zentradi spies who mounted the spy plane in the previous episode - report to Britai and Exsedol on their findings. The Earth refuses to aid the Macross after contact is made for the first time in months. Meanwhile, Quamzin disobeys orders and attacks the Macross radar array, forcing the crew of the ship to send a recon plane to guide them away from the Zentradi.

A TV station is launched on the Macross, and to celebrate, the first ever 'Miss Macross' beauty pageant takes place. Minmay enters, but by doing so she ends up missing dinner with Hikaru on the same night. A Zentradi spy ship approaches the Macross and with Max and Kakizaki on leave, Hikaru intercepts it alone.

As Minmay celebrates her birthday, Hikaru begins to wonder about his relationship with Minmay and emerging feelings for Misa. Hikaru is promoted and has Maximilian Jenius and Hayao Kakizaki assigned as his wingmen. Quamzin mounts another strike against the Macross whilst Hikaru wonders if he'll celebrate Minmay's birthday in time.

After a few months of fighting, the Macross arrives at Mars. Detecting an abandoned base on the planet's surface, the crew land the ship to gather much needed supplies. Quamzin Kravshera, a brilliant but unstable Zentradi commander, attacks the Macross. Meanwhile, Misa requests permission to investigate an emergency signal from within the base.

Using a defensive anomaly left behind after the disappearance of the fold systems, and the rings of Saturn to hide the Macross, Misa and Claudia devise a new attack strategy against the Zentradi.

Zentradi commander Britai Kridanik and his archivist, Exsedol Folmo, begin suspecting that the humans (or 'miclones') are the long-lost 'Protoculture' and send attack waves to test their theory. During a Zentradi attack, Global orders the Macross to "reconfigure" itself to combat mode in order to fend them off. However, the move proves disastrous for the unsuspecting civilians and infrastructure. Roy and Minmay convince Hikaru to join the UN Spacy fleet on the Macross so he could continue flying.

With the fold systems now vanished, Captain Global and his crew come to a realization that the Macross must make a long journey back to Earth. The civilians from South Atalia Island - along with their shops and homes - are brought onto the ship. Meanwhile, Hikaru and Minmay are trapped within the confines of the Macross. Hikaru learns much about Minmay and begins a new friendship with her.

With Hikaru still reeling from the horrors he's witnessed first hand from both sides, events take a turn for the worst when the space folding system of the Macross (a faster-than-light travel technology) teleports it and the city on South Atalia Island to the edge of the Solar system and in front of Pluto.

Air racer and stunt pilot Hikaru Ichijo and his 'sempai' (mentor) Major Roy Fokker attempt a daring rescue mission when South Atalia Island is invaded and bombarded by Zentradi forces. Hikaru has his first encounter with Lynn Minmay, a young waitress, as Zentradi mecha begin raiding the city. Meanwhile, Captain Bruno J. Global, Lieutenant Misa Hayase, Bridge Operator Claudia LaSalle, and the crew of the Macross attempt to launch the ship for the first time.

The story begins in 1999: a giant alien spacecraft crash-lands on South Atalia Island. Humanity proceeds to attempt to rebuild this marvel, but political conflicts centered around the Macross - coupled with proposals for a one-world government - result in a global war. After 10 years, the 'Unification Wars' are finally over, the new United Nations government is in power, with the UN Spacy as their military arm. It's 2009: The work on the Macross is now complete. On the day of launching ceremony, its main cannon fires on its own, destroying an alien spacecraft in orbit. This automatic action marks the beginning of the war between the humans and Zentraedi, a race of humanoid warriors of gigantic size.