Ten years after a mysterious alien ship lands on Earth and is rebuilt with its technology adapted, the alien warrior servants of the ship's owners arrive to retrieve it.
On Minmei's birthday, the newly decorated and promoted Rick Hunter finds himself too occupied adjusting to his new squadron under his command to celebrate it with her.
Rick is ordered to go on patrol, but can't resist watching Minmei in a beauty contest only to find a Zentraedi scout crew who are completely flummoxed by the spectacle themselves.
Upon hearing Lt. Hayes' report, Capt. Gloval decides the ship must return to Earth, while Zentraedi spies are having difficulty infiltrating Macross' incomprehensible civilian society,
With the SDF-1 on Earth, Rick and Minmei and Capt. Gloval and Lt. Hayes go out for separate appointments, only to have less than positive results upon arrival.
After the disaster in Ontario, the SDF-1 is ordered to launch into space as a practical exile. The three Zentraedi spies return and report, sparking curiosity about Micronian mores and music, Minmei in particular.
The grand fleet of the Zentraedi bombard Earth and devastate it while the crew of the SDF-1 and its Zentraedi dissenter allies prepare their retaliation.
In some faraway spot in the galaxy, the Robotech Masters find indication of a giant battle that has taken place in the vicinity of the Earth. They feel this might be the location of their lost protoculture factory.
Finding Lisa depressed at Rick's disinterest in her, Claudia puts her feelings into perspective by telling the story of her relationship with Roy Fokker.
Minmei tries to become part of Rick Hunter's life again after returning from her tour of the frontier. It is a situation complicated by Rick's growing concern for Lisa and his final realization of his duty as a soldier.
The Robotech Masters have finally arrived near the vicinity of the earth. They believe there will be no resistance offered as they try and recover their lost protoculture factory.
In order to accommodate vital military intelligence information, the Supreme Commander of the Army of the Southern Cross asks for volunteers to re-establish communications with an isolated space station.
On a routine patrol, Dana Sterling and Bowie Grant discover a plot by the Robotech Masters to excavate around the site of the final destruction of the SDF-1. Bowie is captured and it is up to Dana to affect his rescue.
The flagship of the Robotech Masters' interstellar armada is hovering menacingly above the earth. It is decided that a direct offensive against the enemy starship is needed.
After successfully disabling the Robotech Masters' flagship, a recon mission is called for. Dana's 15th Squadron is given this dangerous assignment. On the eve of this mission, the soldiers of the courageous squad prepare for battle.
Dana's 15th Alpha Tactical Armoured Corps succeeds in breaching the hull of the fallen alien vessel. They proceed through the gigantic ship in the hope of discovering any information concerning this new threat.
Failing in their attempts at capturing the humans who entered their ship, the Robotech Masters plot to raid a nearby city and capture as many humans as they can in order to experiment and see if they should fear this minor group of creatures.
Dana Sterling tries to get the war with the Robotech Masters out of her mind by attending a concert with Bowie. She meets a singer who she finds interesting only to discover later that he is a spy working for the military police.
The Robotech Masters plan a strange deception by introducing Zor into the ranks of the 15th Tactical Squadron of the Army of the Southern Cross in the hopes of getting some information regarding Earth's knowledge of protoculture.
Zor, the Robotech Master's unsuspecting spy, is subjected to rigorous psychological tests to determine if he is human. Dana cannot allow him to go unchallenged for the destruction he has caused and plans a daring midnight raid on the hospital.
General Leonard is convinced that Zor can help his army get information regarding the Robotech Masters (whether he is human or not). He assigns Zor to the 15th Tactical Squad and places Dana Sterling in charge of his "rehabilitation".
General Leonard calls for an all out attack against the Robotech Masters forces in Earth orbit near the moon. The plan does not include the 15th Tactical Squad, which spends most of its time trying to help Zor regain his memory.