As the prisoner exchange is in progress, a trap set by the Robotech Masters on their ship claims the life of Rolf Emerson. Chaos reigns as the 15th Squad desperately attempts to pull out of the area. Dana tries to relocate Zor while Sean, Marie, Bowie, and the rest of the crew look for Musica's sisters.
Dana Sterling finds Zor determined to personally destroy the Robotech Masters. After a frantic search through the depth of the gigantic ship, Dana and Zor discover the Robotech Masters preparing a new two-front assault against the fleet and the planet.
The aliens do not believe Zor wants to destroy them: "You are the embodiment of Zor, creator of the first protoculture and the Master responsible for our development. It was Zor who developed the Zentraedi people. Zor who became the prime force behind all the advancements of our society. Your most important achievement was the protoculture which brings the promise of eternal life....Surely you are not prepared to destroy your most precious creation, the embodiment of your hopes and dreams? Without it, your native civilization will wither and die."
Zor replies: "My civilization is already dead."
He eliminates one of the three masters. Dana upsets the terminals that control a container of protoculture matrix. She accidentally causes the seeds inside to blossom, releasing their energy. Its usefulness to the remaining Robotech Masters has been destroyed, but for Dana the energy has unleashed racial memories buried within her Zentraedi cell structure. Somehow, Dana finds the strength to reject instincts that urge her to become a part of the Robotech Masters' culture. Hallucinations brought on by the spores leave her half-stunned.
In another section of the ship, Musica leads a battle of her own while the 15th Squad rescues civilian clones – including Musica's sisters – marked for destruction.
"I have freely chosen a new way of life!" Musica tells the sentries. "The truth is, we are all individual beings with free will – and you know it!"
In the ensuring struggle, Octavia is killed. The 15th Squad, with Marie Crystal and Musica, load the surviving aliens into troop carries and evacuate to Earth.
For the Robotech Masters, the moment of retribution is at hand in the form of their rebel clone. Zor kills them. He sets Dana adrift in one of the escape modules, then prepares to destroy the ship. As he locks the controls into a crash-land position over the ruins of the SDF-1, Zor thinks to himself: "There is no other way. The destruction of this ship over the site of the battlefortress is the only guarantee that the protoculture will be obliterated before it brings the Invid to this planet!"
Zor is tragically wrong. His sacrifice only compounds disaster. Instead of rendering the protoculture matrix useless, the explosion frees the mutated spores. They scatter over the planet's surface, turning Earth into a vast, fertile garden awaiting cultivation by the rapidly approaching Invid.
The survivors of the second Robotech War enjoy a bittersweet victory. With morale, supplies, and population depleted, Earth must rebuild once again – this time in the face of another massive invasion they know they cannot win.
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