In the future, humanity has moved out of the solar system and started to colonize planets far away from Earth. One of the farthest colonies in existence is the planet Glorie, on the very edge of explored space. The main military forces protecting the colonists of Glorie from the unknown are the Armies of the Southern Cross.

However, unknown to the human colonists, Glorie is the ancestral home of the Zor, a race of highly advanced humanoids that have been wandering the galaxy for the past few centuries. Although the Zor abandoned their homeworld ages ago, they have now returned with what remains of their fleet to reclaim their planet. Unfortunately, the humans have already made Glorie their new home and refuse to leave it. Since Glorie does not have a large enough food supply to support the humans and the Zor together, they declare war on each other for sole possession of the planet. The resulting war for Glorie basically makes up the Southern Cross TV series. The events focus on Jeanne Francaix (Dana Sterling), the young and inexperienced leader of the 15th ATAC. Jeanne struggles to change her band of misfits and drop-outs into a skilled fighting force, and largely succeeds in turning the 15th ATAC into an elite unit by the end of the war. During the battles Jeanne also grows and matures from a headstrong girl into an experienced woman.

*** Description taken from animenfo.com

Notes about Robotech Masters
Robotech Masters is the butchered US version of Southern Cross done by Harmony Gold. It was dubbed, heavily edited and the plot was completely rewritten.
Aside from the very first episode of Robotech Masters (Episode 37 of Robotech global) the actual episodecount remained, as did the rough episodestructure. Episode 37 was cut together from bits of Macross and southern cross to fill the gap of inconsistences.