The story begins with a young Emma Rodman recalling a triumphant return of the Banfield family's fleet to their home planet, Hydra. She remembers the awe-inspiring sight of massive warships and humanoid robots called "Mobile Knights" filling the sky, a symbol of their lord, Liam Sera Banfield, having defeated the fearsome Goaz Space Pirates. This memory fuels her childhood dream of becoming a Mobile Knight herself to protect others.
Thirty years later, Emma, now a Lieutenant Junior Grade, has achieved her dream. However, her first combat mission as a pilot of the Banfield family's standard Mobile Knight, the Nevan, is fraught with difficulty. She struggles with the machine's sluggish response, despite pre-flight checks showing no issues. Her instructor, Claudia Bertrand, a highly skilled "AA" ranked knight, reprimands her for her erratic piloting. During the engagement against space pirates hiding in an asteroid field, Emma hesitates to deliver the final blow to a defeated enemy, a stark contrast to the brutal efficiency of her comrades. Her hesitation is met with harsh criticism from Claudia, who emphasizes the necessity of fulfilling her mission.
After the mission, Emma receives a devastating "D" rank evaluation, the lowest possible, for her inability to pilot effectively and her failure to kill a surrendered enemy. Claudia, a stern and experienced officer who herself suffered a past trauma involving incompetent allies, dismisses Emma as useless, stating that the Banfield family, facing a shortage of knights after a recent war, cannot afford such incompetence. Despite this, Emma, fueled by her childhood dream and a desire to protect the weak like Lord Liam, resolves to improve.
Assigned to the aging aircraft carrier Melea, Emma finds herself in a unit filled with unmotivated personnel, including the cynical pilot Larry Kramer and the pragmatic mechanic Molly Barrel. The Melea is a relic of the old Banfield private army, now relegated to escort duty for survey missions to newly acquired, undeveloped planets like Elias. The crew's lack of discipline and the ship's outdated equipment contrast sharply with Emma's earnest desire to be a knight.
During a survey mission to Elias, Emma's unit is attacked by space pirates using modified Mobile Knights called Zorks. Emma's own Mobile Knight, an older model Nevan designated "Moheav," proves difficult to control, mirroring her initial struggles. Despite her subordinates' apathy and the disdain of other units, Emma, driven by her ideals, intervenes to protect the survey team, even using her Moheav in a reckless charge. This act, while seemingly foolish, demonstrates a surprising aptitude for piloting the difficult machine, albeit with significant damage.
Meanwhile, intelligence reveals a pirate weapons manufacturing plant on Elias. Claudia Bertrand, now a Colonel, is dispatched with a specialized unit, the "Jaeger Corps," to destroy it. The mission is complicated by the discovery of the plant's true purpose: it's a trap orchestrated by a mysterious individual named "Mr. River," who seeks to damage the Banfield family's reputation by orchestrating the defeat of their elite forces.
The Banfield forces, including Claudia's Jaeger Corps and the hastily assembled Melea crew, launch an assault. The pirates, led by River, reveal a massive underground weapon, "Big Bore," capable of overwhelming the Banfield forces. While Claudia's elite unit fights valiantly but struggles against the Big Bore, the Melea crew, initially reluctant, is drawn into the conflict. Emma, piloting a newly assigned, experimental Nevan custom model named "Atalante," proves surprisingly adept at maneuvering the highly sensitive machine, her piloting style finally matching its capabilities. She manages to damage the Big Bore's power source, allowing the ground forces to disable it. The battle concludes with the pirates defeated and their plans thwarted, though the true mastermind, River, escapes. The events highlight the stark contrast between the disciplined, elite forces of the Banfield family and the dilapidated, unmotivated remnants of their older military structure.