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.

The final battle of the Second Robotech War is fought as Zor goes on the rampage to destroy the entire culture created by the Robotech Masters before the arrival of the Invid. His plan fails, causing his destruction and paving the way for the Invid to cultivate the flowers of life that are now seeding the planet and turning the earth into a protoculture greenhouse.

The battle between the Robotech defenders and the Zentraedi is taken tot he very limits of the Solar System as the two forces meet in the rings of Saturn.

Zor and the rest of Dana Sterling's 15th Tactical Squad make a daring trip to the Robotech Masters' flagship in order to rescue General Rolf Emerson, Bowie's guardian, and try and put a stop to the second Robotech Wars.

Nova tracks Bowie and Musica to the crash site of the SDF-1 and makes a startling discovery in regard to the nature of Protoculture and the growing threat of the impending Invid invasion. Zor realizes that the Robotech Masters must be stopped at any cost.

Musica tries to assimilate herself into the "alien" environment she finds on earth. Her joy of discovery in this new world is cut short when Nova Satori, the military police, seeks her out as a spy. Bowie and Musica become a fugitive couple to avoid capture.

A critical battle takes place aboard the Robotech Master's Flagship, as Zor and Musica, a Robotech clone mistress, defect and join the earth forces. A daring escape forms the basis of the new relationship between Zor and members of the 15th Squad.

Trying to escape from the Robotech Masters, Dana and her friends discover many secrets concerning the true nature of the civilization living aboard the flagship of the Robotech Masters and the entire process of biogenetic engineering.