"Armored Trooper Votoms" is set in a distant future where humanity has colonized multiple star systems, leading to a fractured galaxy dominated by warring factions. The story centers on Chirico Cuvie, a former elite soldier known as a "Red Shoulder," who becomes embroiled in a complex conspiracy after being betrayed by his superiors. The narrative begins with Chirico being sent on a mysterious mission to retrieve a secret cargo, only to discover that the operation was a setup. This betrayal sets off a chain of events that forces him to go on the run, pursued by both military forces and shadowy organizations.

As Chirico evades capture, he uncovers the existence of a secret project involving genetically engineered super-soldiers known as "Perfect Soldiers." These soldiers, created through advanced biotechnology, are central to the ambitions of various factions vying for power. Chirico’s journey takes him across multiple planets and through intense battles, often fought using Armored Troopers (ATs), the series' signature mecha. These humanoid combat machines are versatile and heavily utilized in the galaxy's ongoing conflicts.

Throughout the series, Chirico encounters a diverse cast of characters, including allies and adversaries who shape his path. Among them is Vanilla Vartla, a resourceful mercenary; Gotho, a seasoned veteran with a knack for survival; and Fyana, a mysterious woman who is revealed to be one of the Perfect Soldiers. Chirico’s relationship with Fyana becomes a key emotional driver of the story, as he seeks to protect her from those who would exploit her abilities.

The plot is divided into distinct arcs, each exploring different aspects of the galaxy’s political and military landscape. From the war-torn planet of Uoodo to the harsh desert world of Sunsa, Chirico’s quest for answers and survival is marked by relentless action and strategic combat. The series delves into themes of identity, loyalty, and the cost of war, with Chirico’s personal journey serving as the narrative backbone.

As the story progresses, Chirico’s pursuit of the truth leads him to confront the creators of the Perfect Soldiers and the broader implications of their existence. The final arcs reveal the extent of the conspiracy and the role Chirico himself plays in the larger scheme. The series concludes with a resolution that ties together the central mysteries while leaving room for contemplation about the future of its characters and the galaxy they inhabit.