In 1999, an alien ship crashes on South Atalia Island. Humans then know that they are not alone in space. Ten years later the ship has been rebuilt and named the SDF-1 Macross. However, on the day of its take off, a species called the Zentraedi arrive at Earth, beginning the UN Spacy vs. Zentraedi war that forever changes the history of these two species.
An abandoned alien battle fortress crash-lands on Earth in 1999, stopping a world war in the process. The international scientific community spends the next ten years reconstructing the damaged ship, called the SDF-1. At the ship's launch in 2009, a race of giant alien warriors, the Zentraedi, appear and attack Earth in a bid to capture the vessel. Young sport pilot Rick Hunter has his first experience with a rather odd fighter plane.
The Zentraedi troops assault Macross Island to capture the SDF-1, which fails a liftoff attempt. After witnessing the transformation of his Veritech fighter plane, Rick rescues a young girl named Lynn Minmei.
The SDF-1 successfully flies off Macross Island to link up with other Earth forces in orbit. A Zentraedi ambush forces SDF-1 skipper Captain Gloval to go back to Macross Island and attempt a hyperspace jump. The consequences of the jump turn out to be totally unexpected. Meanwhile, Rick tries to bring Minmei back to her family, but crashland in a section of the SDF-1.
Rick and Minmei try to survive inside the uncharted space of the SDF-1 where they crash-landed, but are eventually stumbled upon and rescued by construction crews assigned to rebuild Macross City inside the ship.
Having been rescued from the fallout shelters of whatever is left of Macross Island, the citizens attempt to normalize their life aboard the giant battle fortress. Roy Fokker encourages Rick to join the Robotech Defense Force. The SDF-1 crew discover that the spacefold drive they used to make the jump has disappeared, but stumble upon an idea to transform the ship. The idea is soon tested in a battle with the Zentraedi, but renders much damage to Macross City.
The SDF-1 crew rebuilds Macross City once more to take the transformation into account. Rick takes up Roy's advice and joins the Robotech Defense Force, which plans to break through the Zentraedi blockade at Saturn's rings.
The SDF-1, transformed back into ship mode once more, arrives at a human outpost on Mars to gather fresh supplies, but discover that the base was damaged in a battle years before and had no survivors. However, the Zentraedi lie in wait with a new commander, Khyron, raring for glory by using gravity mines to trap the ship. In the midst of the fight, SDF-1 First Officer Lisa Hayes tries to find out whether her old fiance, Carl Riber, is still alive.
Awarded a medal for saving Lisa in Mars, Rick is promoted to lieutenant and introduced to his new wingmen, Ben Dixon and Max Sterling. However, an attack by Khyron distracts him from another thing on his mind - attending Minmei's 16th birthday.
Minmei joins the Miss Macross pageant while Rick Hunter is sent on patrol. The Zentraedi use the opportunity to study human culture further by sending a reconnaissance craft to tap on the pageant broadcast.
An unauthorized assault by Khyron on an asteroid damages the SDF-1's radar systems, forcing Lisa to go on a scout mission with Rick, Max, and Ben protecting her. The Zentraedi ambush Lisa and brings her to Breetai's flagship, where the three pilots come face to face with Breetai himself.
Rick, Lisa, and Ben are captured and brought before Zentraedi leader Dolza. They witness the awesome power and destructive capability of their alien adversaries, but also discover their captors are mysteriously disturbed by something entirely different. Minmei's victory in the Miss Macross pageant opens many opportunities for her.
Held captive in a Zentraedi prison cell, Rick, Lisa, and Ben try to figure a way off the massive alien ship. With his fighter still intact, Max sneaks his way through the Zentraedi ship and finds his comrades. A fierce gunfight allows the humans to find a battlepod and return to Captain Gloval and the crew of the SDF-1. Because the humans escaped on his watch, Breetai is relieved of command and replaced with Azonia. The three pilots who observed the Miss Macross pageant - Rico, Konda, and Bron - volunteer to be micronized and infiltrate the SDF-1 to gather more intelligence about the humans.
Rick, Lisa, Max and Ben are debriefed regarding their capture by the Zentraedi. Azonia stops Khyron from attacking the SDF-1 again, allowing the crew to safely reenter Earth's atmosphere.
While the SDF-1 passengers and crew celebrate their arrival, Captain Gloval makes his recollections on the SDF-1's journey across the Solar System.NOTE: This episode is a clip show that recaps the previous 13 episodes.
Rick secretly flies Minmei to Japan to visit her family in Yokohama, but things go sour as Minmei defies her parents' wishes to stay with them. Her pacifist cousin, Lynn Kyle, offers to watch over her as they fly back to the SDF-1. Meanwhile, Captain Gloval and Lisa Hayes fly to the United Earth Government's (UEG) headquarters in Alaska to be debriefed on the voyage and the Zentraedi's battle capabilities. However, they discover that the UEG leadership covered up the SDF-1's spacefold jump, claiming to the world that anti-unification rebels detonated nuclear weapons on the place.
Lynn Kyle's presence suddenly reminds Lisa of her lost fiance, Carl Riber. Khyron executes another attack on the SDF-1. The human forces beat back the Zentraedi, but Lisa's execution of the Daedalus Maneuver catches Rick in the crossfire.
Wounded from the attack in the previous episode, Rick Hunter lies in a hospital bed in critical condition. At the same time, he experiences dreams that try to make sense out of his relationship with Minmei and his growing attraction to Lisa Hayes.
As Rick recuperates, Roy tries to convince Minmei to take a break from her busy schedule and visit her friend. A female Zentraedi power armor pilot named Miriya is intrigued by Khyron's hints about a human ace pilot who could be more of a match for her and sets out to find him. Roy prepares to go into battle... perhaps for the last time.
After broadcasting appeals for a safe haven, Captain Gloval receives an offer from Toronto, Ontario Quadrant in Canada about accepting the SDF-1's 56,000 refugees while planning a test of a new omnidirectional barrier shield. A sudden attack by the Zentraedi overloads the barrier system and destroys the alien force, but it also kills Ben and lays waste to an entire city below the battle fortress.
The fallout from the previous episode's battle forces the United Earth Government to banish the SDF-1 from the planet with the necessary supplies to send them on their way. Shocked by the battle's outcome, Zentraedi leader Dolza gives Breetai a million-ship fleet to deal with the SDF-1. The Zentraedi spies - Rico, Konda, and Bron - escape the vessel and report back to Breetai on their mission. After seeing Captain Gloval break down while announcing the UEG's banishment order, Minmei comes to his side and encourages the people and crew of the SDF-1 to pull themselves together.
Minmei and Lynn Kyle's first movie, Small White Dragon, becomes the talk of the town, as crowds gather for the premiere. Left unease by the cousins' love scenes, Rick and Lisa walk out of the movie theater. An unpleasant accident results in the two of them taking a walk together, but the bond grows closer in the midst of the SDF-1's latest transformation during a Zentraedi attack. The Zentraedi themselves are also disturbed by the movie, especially when they think Lynn Kyle's fight stunts indicate superhuman abilities.
Khyron personally leads another attack on the SDF-1 while Breetai, Exedore, and Dolza discuss their next action against the humans. However, Rico, Konda, and Bron's retelling of their experiences aboard the ship encourages their fellow Zentraedi soldiers to defect. The SDF-1 tries a Daedalus Maneuver on Breetai's flagship, where the Zentraedi breaks through the Destroid force to enter the SDF-1 and wreak havoc. Yet, through all the fighting and confusion, Minmei still manages to sing for the bewildered citizens of Macross City, giving them a small ray of hope in their darkest hour.
The battle inside Macross City rages and Khyron appears to carry the day at last - until many of his soldiers suddenly desert and try to find Minmei. The Zentraedi defectors are given political asylum.
Lisa Hayes returns to Earth and try to convince the United Earth Government - especially her father - to negotiate with the Zentraedi armada. Later at a video arcade, Miriya, who has infiltrated the SDF-1, finally comes face-to-face with the ace pilot she has been intrigued with for a long time - Max Sterling, who proves to be a powerful opponent.
Euphoric over his arcade victory, Max asks Miriya out for a date, but defeats her a second time after she tries to kill him, which eventually results in the two of them getting married. Touched by the footage of the wedding, more Zentraedi within Breetai's fleet openly refuse to launch another attack against the humans, as Dolza directs their immediate destruction.
An uneasy truce is called as the Zentraedi send a micronized Exedore to the SDF-1 for peace talks. This move not only shocks the citizens of the SDF-1, but also fuels the already smoldering fires of ambition in Khyron.
Concerned by the growing numbers of Zentraedi soldiers who have been exposed to human culture, Dolza's main armada finally appears and lays waste to Earth. Despite the carnage, Rick encourages Minmei to rally the SDF-1 and its newfound Zentraedi allies in a battle against Dolza's forces.
Two years after the battle for Earth, the crew of the SDF-1 take stock of the devastation and begin to pick up the pieces.
The Robotech Masters learn of the SDF-1's location and prepare for a journey to Earth. Meanwhile, some Zentraedi who are tired of civilian life have returned to their military ways. Khyron, who has been dormant since the big battle for Earth, reemerges to rally all Zentraedi forces who want to carry on the fight against the humans.
The survivors of the SDF-1 and Breetai come together to convince a Zentraedi force at a Robotech Factory to join in an alliance for peace. Max and Miriya bring along their baby, Dana, to press their point. Elsewhere in the galaxy, the Robotech Masters, lamenting on the defeat of the Zentraedi, discuss how to clone Zor, the creator of Robotechnology.
Khyron begins his campaign by hijacking the last existing Protoculture chamber in New Detroit to help more micronized Zentraedi get back to their original size. Captain Gloval and Exedore study the origins of the Zentraedi and learn more about the Robotech Masters.
Khyron's forces assault a Minmei concert and take the singer and Lynn Kyle hostage in exchange for the SDF-1. Rick and Lisa spearhead a rescue mission.
Lisa is distraught over Rick and Minmei's mutual feelings for each other. To cheer her up, fellow bridge officer Claudia Grant brings her to her quarters and recounts the story of how she met Roy Fokker.
Rick invites Lisa to a picnic, but his detour to meet Minmei at Monument City - and a subsequent Zentraedi attack at a nearby base - ruins what should have been their perfect time together. Minmei, on the other hand, is fed up with Lynn Kyle's interfering in her affairs and parts ways with him after her concert the same day, where she refused to sing.
Lacking enough power to fully energize a derelict Zentraedi Gun Destroyer lying in the Amazon rainforest, Khyron plans an attack to capture the Protoculture Matrix on the most unusual of days - Christmas Day. Having decided to end her music career, Minmei comes to the only person she could possibly spend the holidays with.
Emboldened by the Protoculture Matrix powering his battleship, Khyron takes one last stab at the SDF-1. Lisa considers resigning from the service until Admiral Gloval assigns her to lead the mission to find the Robotech Masters. The resulting battle finally affirms Rick's feelings for Lisa, but Minmei is left hanging.
The United Earth Forces Military Academy produces its first batch of officers for the Army of the Southern Cross, including 2nd Lts Dana Sterling and Bowie Grant. Bowie is uneasy about being commissioned into the armed forces, but Dana helps him get over it by telling the story of how her famous parents met. The narration is interrupted by the in-system appearance of the Robotech Masters after a 15-year trip.
Dana is thrown into the brig after running afoul of Tactical Armored Space Corps (TASC) officer First Lieutenant Marie Crystal but is released in time for the Southern Cross' first ground-based encounter with the Robotech Masters. The aliens are caught by surprise at the human forces' capabilities. Dana's skills during the battle earns command of the 15th Alpha Tactical Armored Corps (ATAC) after its commanding officer, Captain Sean Phillips, is demoted to private second-class for flirting with a colonel's daughter. Dana is intrigued by visions of a red Bioroid and its pilot.
The 15th Squadron is assigned civil defense duty during an aerial offensive. Dana initially laments the posting, especially when she sees the Masters' counterattack fall upon her base but proves her worth when she orders the 15th ATAC into action. Dana is promoted to first lieutenant after her team repulses the aliens.
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Answering a call for volunteers, Dana and members of the 15th ATAC join forces with Marie Crystal in an operation to reestablish communications with Space Station Liberty, which lost contact with Earth shortly after the Robotech Masters' arrival.
Dana and Bowie stumble into an excavation operation by the Robotech Masters in the remains of what was once New Macross City, centered on the earthen mounds that hold the remains of the SDF-1, SDF-2 and Khyron's battlecruiser. Bowie is captured. Enraged by her superiors' refusal to authorize a rescue operation, Dana fakes a late-night training exercise to launch the mission herself.
An impulsive frontal assault ordered by Supreme Commander Anatole Leonard against the Masters' flagship results in the Southern Cross Tactical Armored Space Corps (TASC) hit with heavy losses. Corporal Louie Nichols, one of Dana's troopers, theorizes a potential weakness, and Dana gets approval for a different tactic. Their subsequent attack succeeds in bringing the flagship down to Earth. Meanwhile, Earth scientists study the remains of a Bioroid pilot and discover that the intruders are human, not micronized Zentraedi.
The 15th Squadron's successes make them the military's talk of the town as they are selected for another dangerous mission. The unit is hampered by Bowie's behavior, which has caused him to be arrested twice by Global Military Police (GMP) Lieutenant Nova Satori. Dana decides to leave him to his fate, but his guardian, General Rolf Emerson, intervenes to get him out of the stockade in time for the mission to begin.
The 15th ATAC penetrates the Robotech Masters' flagship, where Bowie encounters a beautiful alien woman who shares his love for music. The Masters entrap the team, but they fight their way out, capturing an enemy Bioroid in the process.
The Southern Cross High Command reviews the footage of the 15th Squadron's reconnaissance of the alien ship and concludes that the Robotech Masters are probably after the remains of the Protoculture Matrix. Commander Leonard rules out negotiations with the aliens. The Masters are frustrated by their failures to clone Robotech genius Zor and consider getting humans as test subjects.