The Robotech Freedom Fighters led by Scott Bernard discover the deserted remains of Denver, Colorado. They go through the empty streets looking for supplies and trying to enjoy a moment of relative peace from their constant struggle against the Invid. Scott begins to feel a tug of emotion towards Marlene.

The group finds themselves in a high desert ghost town populated by an assemblage of old timers who have Robotechnology. The return of the newest attack wing of the Robotech Defense Forces, now personally headed by Admiral Rick Hunter, sends a call to glory into the lives of many who have lost the will to fight. Scott and his friends learn the true meaning of courage.

On a snow-capped mountain pass, Scott Bernard and company defend themselves against a massive attack by the Invid, led by Sera, who is torn between her loyalty to the Regiss and her uncontrollable emotional instability which she feels as a result of transforming into a human. Sera confronts Marlene with the realization that she is not human, but an Invid.

The Regiss, Queen of the Invid, allows two of her children to transform their protoplasmic bodies into humans as part of the process of finding the ultimate life form. Sera and Corg, take this opportunity to hunt down the humans who have proved to be a thorn on the side of their mother, the Regiss, from the beginning of their arrival on Earth.

Following Annie's departure from the group, a sense of melancholy settles over Scott and his friends. Petty arguments get blown-out of proportion and the group decides to split up. An attack by the Invid unites the group once again and the return of Annie (who has left her native "Prince Charming" to rejoin her friends) makes the group stronger than ever in their resolve to destroy the Invid and Reflex Point.

While traveling through a forest of mature trees that were once active Invid Flowers of Life, Scott Bernard's group is captured by a tribe of outcasts. They have canonized the Invid as their sacred protectors and only through the intervention of Scott and his friends are these humans able to accept their humanity and fight back against their alien enemies. Annie gets a crush on a young tribal prince and decides to become his jungle princess.

Rand tries to find water for Marlene who has grown ill following the destruction of the Invid Fortress. He braves a sandstorm that circulates many of the spores of the Invid Flower of Life that overwhelm Rand and induce a strangely prophetic dream about the nature of the Invid and their purpose in invading the Earth.

In order to continue on to Reflex Point, Scott Bernard and his friends must first destroy an old Robotech Fortress that is now occupied by the Invid. The group separates and infiltrates the complex and manages to destroy the Invid stronghold. Then they blast a trail to freedom for themselves and the rest of the citizens living in fear of their alien conquerors in this area.

The intrepid band of freedom fighters come upon a thriving community which makes its living by selling information to avoid the Invid and migrate to a new and wonderful Utopia just over the mountain. Sounding too good to be true, the heroes investigate and expose the evil plot of the town's mayor. Lancer also takes time to visit with an old friend.

The Invid send a "simul-agent" into the midst of Scott Bernard and friends in order to find out how much this band of freedom fighters knows about them and their plans. The Invid plan backfires when Rand discovers the Simul-agent before the transformation process is complete. This creature, an Invid that resembles a woman, joins with the group as they continue their journey to Reflex Point.

The Zentraedi plan an ambush for the SDF-1 at a deserted Martian Outpost.

Scott, Rand and Annie are separated from the group and find themselves in a Genesis Pit. It is an experimental lnvid Laboratory in which these strange aliens are conducting genetic experimentation on Earth biological history – they are creating dinosaurs and ancient animals in the search for the perfect life form.

Scott Bernard and his band of comrades come upon a force of Robotech Defense Forces under the command of one of his childhood heroes, Col. Wolfe. When Scott offers the services of his group to aid in Wolfe's plans to defeat the Invid, Scott finds himself double-crossed by a hero who has lost his courage under the pressure of the Invid.

Lunk is on a mission to deliver a manuscript to the father of one of his dead comrades. It was a promise he made and feels honor-bound to keep. A hostile reception by the local townspeople forces Lunk to re-evaluate the nature of friendship and duty.

Rook Bartley is reminded of the past as the band of freedom fighters powers their way through Rook's hometown. Rook takes the opportunity to look up her family and try to settle some old scores with a gang of thieves who humiliated her several years earlier.

Yellow Dancer stages a rock concert to serve as a diversion allowing Scott Bernard and his band of Freedom Fighters a chance to sneak into a Protoculture Storage Area and confiscate valuable fuel needed to power their Alpha Fighters and Cyclones.

The group of freedom fighters, now joined by Yellow Dancer (aka Lancer), Rook Bartley (a brave young woman) and Lunk (aka Jim Cooper), try getting back to nature as they set-up a base in the center of a hostile forest under the constant scrutiny of Invid Scout Troops and Invid Shock Troopers.

Scott, Rand and Annie, a precocious 13-year-old girl, try to help some citizens in a remote town fight off a gang of thugs and an attack by an Invid Scout Patrol. This episode introduces the cast to "Yellow Dancer," a pop rock star who tries to entertain the survivors in the tradition of Lynn Minmei.

Scott Bernard, the sole survivor of the Robotech Expeditionary Force's ill-conceived attack against the Invid stronghold known as Reflex Point, joins forces with Rand, a young rebellious freedom fighter, as they try to recruit an army of Earth's survivors to carry on the fight against the Invid.

The Robotech Expeditionary Force returns to Earth in the wake of the invasion of the Robotech Masters only to find their planet completely overrun by an alien life form known as the Invid.