Fifteen years after the destruction of SDF-1 and SDF-2 and the Zentraedi holocaust, Dana, the daughter of Max Sterling and Miriya, is among the first graduates of the United Earth Forces Military Academy. The academy is an oasis of order and optimism on the ravaged planet, by the mood changes when the Robotech Masters arrive from far space in pursuit of their lost protoculture factory.

Now the pilots are on emergency alert. Dana is bright and spunky, and she manages to get herself thrown in the brig because of her escapades. But she gets out in time to shine when she leads her squad into battle with the Robotech Masters. The aliens are surprised by the Earthlings' bold defense, and the first encounter ends with neither side victorious.

As the Robotech Masters continue their attacks, the Earth goes on alert for war. Dana Sterling is assigned to a defensive postition, away from the action. When she sees the main base is in jeopardy, she enters the fight and changes the course of the battle, forcing the bioroids away.

Acclaimed as a hero and promoted, Dana volunteers for an even more dangerous mission - reestablishing control of Space Station Liberty. With fellow volunteer Marie Crystal, Dana flies to the orbital station, where she wages a furious battle to free the base and comes face-to-face with the red bioroid which has been haunting her dreams. The alien invaders fight fiercely to hold on to the vital communication link, testing the abilities of Dana and Marie.

When Dana and Bowie engage an advance party of Robotech Warriors in a fiery skirmish near the ruins of New Macross City, Bowie is captured. The aliens are excavating the crash site of SDF-1 - backed up by a massive bioroid attack. Dana, circumventing her orders, mounts a dangerous rescue operation while Bowie attempts his own escape.

Trying to avoid a battle on Earth, Supreme Commander Leonard sends the Global forces into space to attack the enemy, but the result is a disaster, with many killed and captured. Again, Dana and the 15th Squad must come to the rescue, using an untried plan to disrupt the workings of the huge Robotech Fortress. With the fates of the prisoners and possibly all of Earth in the balance, Dana and the 15th roar into battle against the Robotech Masters.

As Dana and the 15th Squad prepare for a reconnaissance mission on the downed alien battle fortress, Bowie Grant is arrested twice by the Global Military Police in an off-limits music club. His desire to play the piano lands him in a cell just when the rest of the squad leaves for its assignment. Bowie is freed in time to join his comrades as they penetrate and explore the ominous alien battleship - secretly observed all the while by the Robotech Masters.

Their discoveries include a high tech biomechanical android factory and Musica, a mysterious and beguiling woman who plays a cosmic harp. By the time they realize they are in a trap, the 15th Squad is locked in jeopardy deep within the deadly fortress.

Examining a captured bioroid, the Earth Forces struggle to unlock the nature and motives of the Robotech invaders. Risking her position, Dana objects to a plan to kill the opposing pilots - she feels a strange kinship with the aliens. Meanwhile, the Robotech Masters are eager to regain the protoculture matrix before another alien race, the Invid, reaches Earth. They decide to take human prisoners to probe their knowledge and usefulness.

Combat rages through the city as the invaders seize Earthling and the Global Command counterattackes. Dana carries out a desperate mission to destroy the Robotech ship, but when the aliens receive help from their hidden armada, her plans go awry.

Zor Prime - an enemy bioroid pilot suffering from amnesia is captured by the Global Forces. They think he is an Earthling forced into service, not realizing that he is a clone of the genius who invented Robotechnology, and that the Robotech Masters have implanted controls in him. As the military police probe and study Zor Prime, the aliens are aware of their every move. Dana's half-alien parentage continues to cause her confusing feelings and strange dreams. Bowie cannot stop thinking about Musica, the alien harpist. But their personal problems are small when compared to the frayed defenses of Earth.

A reconnaissance mission from SDF-3 fights through the alien war fleet and is rescued by the 15th Squad, only to bring word that no aid will be coming.

The captured alien Zor Prime is made a member of the 15th Squad, which delights Dana, but not all the others. She enjoys training the exceptional new recruit and feels a kinship with him. With their secret control of Zor Prime, the Robotech Masters are able to observe military plans made on Earth. When Commander Leonard, despite opposition from some, throws the Earth forces into a full-blown battle, they take advantage of their knowledge.

In a fiery clash, the human forces must struggle against a superior enemy. The 15th Squad is left out of the battle. Instead they take Zor Prime to the buried wreck of the SDF-1, where the eerie remains and strange growths stimulate his memory of his mysterious previous life.

The Robotech Masters' supply of protoculture is dwindling, causing their bioroids to malfunction and their enemies, the Invids, to draw closer. Still, their remaining forces, aided by intelligence unknowingly supplied by Zor Prime, are formidable. They keep the combat pressure on Air Cavalry One, led by Lieutenant Marie Crystal, which has been sent to rescue the defeated Earth attack fleet. Supreme Commander Leonard plans a second offensive against the aliens and places General Emerson in charge. Emerson opposes Leonard and knows that the mission is perilous, but he assumes his duty and prepares for the struggle.

Military Intelligence searches for the source of the continuing leaks, without success. Marie keeps up her pursuit of Sean, and finally gets what she wants - a date. Unfortunately, things aren't always what they seem, and the evening takes a bewildering turn.

While playing video games with the other member of the 15th Squad, Louie devises a system for targeting weapons with eyesight. He and Dana develop the device for training purposes, but when the military used it for combat, Louie revolts and tries to destroy his creation.

The Earth Defense Fleet, under General Emerson, needs Louie's invention for the titanic struggle against the Robotech Masters. Both sides unleash massive forces and the balance swings back and forth. Zor Prime rallies Dana and the 15th Squad as their attack blasts and penetrates the enemy command ship. But, when victory seems at hand, the alien commanders reactivate their hidden neurosensor in Zor Prime and the brave warrior for Earth again becomes a pawn in their game.

Pursued all the while, Dana and the 15th Squad range through the Robotech Masters' command ship, discovering many of the secrets of life in this complex alien civilization. The advanced biotechnology allows complete control of the cloned population - but contact with humans and their emotions has an unsettling effect on them. Bowie finds Musica, the alien woman who has haunted his thoughts. He is able to help her unlock the emotions hidden within her and she rebels against the cold-hearted Masters.

With Musica's help, Zor Prime also overcomes the mental control of the alien masters and rejoins his human friends. Now the challenge is to escape from the huge ship as the Robotech Masters fight furiously for control. And Zor Prime, now neither programmed clone nor human, must find his own destiny

Musica returns to Earth with the 15th Squad and the rest of the attack fleet, but Nova and the military police think that she may be a spy. Bowie and Musica flee to the ruins of SDF-1, where the protoculture has been invaded by the Invid "Flower of Life," forerunners of an enemy alien race. With the Invid flowers also depleting the protoculture aboard their command ship, the Robotech Masters are losing control of the clone population.

Desperate, they plan an all-out effort to seize Earth's supply of Protoculture. Their attack will be met by an equally furious campaign led by Emerson. Zor Prime regains his memory of the past when he sees the Invid flowers in SDF-1 - now the true nature of protoculture and the Invid threat can be explained.

The second Robotech War reaches a climax as the Robotech Masters and the Earth Forces meet in total combat. The aliens take brutal steps in a desperate fight for survival, while the humans struggle against their huge armada. As he maneuvers to defend Earth, Emerson is captured.

The survivors of the 15th Tactical Squad plan a daring mission to thwart the plans of the Robotech Masters, who have virtually crippled the United Earth Government defense forces. The young heroes come face to face with the dreaded Robotech Masters in a no-win situation, which must be faced if the Earth is to survive.