Commander Takuto Meyers is a commander of the 2nd Frontier Fleet, when exiled Prince Eonia launches his coup, Most of the Royal Family on the homeworld were killed via orbital bombardment, and large portions of the Imperial Fleet were destroyed in the surprise attack. As Commander Meyers is unable to contact 2nd Fleet HQ, he waits on standby for orders, until three members of the Angel Wing arrive, with a large fleet chasing them, which turns out to be unmanned ships. After destroying the fleet, Meyers takes his fleet and follows them back to where the Elsior is hiding, the battleship usually used only by the Imperial Guards for ceremonies and meets his old Instructor Lufte, now Commodore, who charges Meyers with commanding the Elsior and the Angel Wing in escorting Prince Shiva, the only survivor of the Royal Family, to the Rhombe system where loyalist forces are gathering for a counter offensive as the 2nd fleet has already been destroyed. Before the engines can be repaired however, more enemy ships arrive, and rather than risking discovery, COmmodore Lufte takes command of the remaining fleet and draws the enemy ships away, while the Elsior remains and makes its way to Rhombe, fighting off enemy attacks along the way, including elements of the Imperial Fleet changed sides to side with Prince Eonia.
While attempting to meet up with the 3rd fleet stationed at Rhombe, the Elsior discovers destroyed remnants of the 3rd fleet and runs into a trap by Prince Eonia's main fleet. While fighting the forces, they receive another message from the 3rd fleet with a new rendezvous point, after fighting their way through the enemy fleet to the rendezvous point, allied reinforcements arrive and force the enemy forces to retreat, Commodore Lufte having evaded enemy forces and reached the Rhombe System ahead of the Elsior. Afterwards, the Loyalist fleet launches an operation to destroy Prince Eonia's main fleet at the Nadler system, and they inflict a serious defeat on the enemy and the commanding admirals(and other high ranking officers of the Imperial Navy) decide to hold a ball in Prince Shiva's honour, and plan to transfer Meyers away to command another fleet while the Angel Wings and the Elsior remain behind to guard Prince Shiva on Fargo, an orbital city around the planet Rhombe. On a routine visit to the ship's hangar, Meyers bumps into a strange girl called Noah, who wants Meyers to give him one of the Emblem Frames. When Meyers refuses, Noah gets angry, says that she will make more and stronger ones, and runs off, disappearing just around the corner. Shrugging the incident off, Meyers takes his chosen love with him to the ball, and while there Prince Eonia shows up with several soldiers to try and take Prince Shiva into his Custody, although Prince Shiva refuses. Shots are fired, and it is revealed that Prince Eonia and the soldiers are just holograms and are not physically present, at this point Eonia's fleet launches a sneak attack while most of the Loyalist fleet is docked and not combat ready, and inflicts serious damage on the port facilities.
Meyers heads back to the ship with Prince Shiva, and after the enemy fleet retreats, the Black Moon, an identical counterpart to the White Moon(a planet sized structure) shows up and fires a massive laser that slices Rhombe in half and destroys much of Fargo and the Loyalist fleet. Meyers and the Angel Wing fight a desperate battle to reach the Black Moon, which is constantly producing attack satellites and unmanned ships, before Noah unleashes an EMP like blast that leaves the Elsior, the Emblem Frames and the Loyalist Fleet powerless except for sensors and communications, before attacking them as they lay helpless. While the situation looks grim, suddenly the Elsior and the Emblem Frames have their power restored to above their original levels, and the Emblem Frames all grow wings. They manage to break through the defensive line and damage the Black Moon which causes Prince Eonia to back off for now, turning it into a stalemate, although afterwards the Emblem Frames lose their wings and their power levels drop to below normal.
As the loyalist fleet gathers on the other side of Rhombe, Commodore Lufte takes command as everyone higher ranking was MIA and presumed dead. Elsior's chief engineer, Creta and Prince Shiva shed some light on the abilities of the Elsior and the Emblem Frames, and also that there is a weapon possibly capable of destroying the Black Moon, but it is stored in the White Moon. While briefing Commodore Lufte on the situation, he mentions that Noah was spotted on other ships and the port facilities before the attack, although when guards attempted to question her, she disappeared into smoke right before their eyes. The Elsior and the Loyalist fleet then head to the White Moon in order to retrieve the weapon, as Sherry, Prince Eonia's second in command, tries to stop them along the way, but fails, finally sacrificing herself as she tries to ram her flagship into the Elsior, although the Angel Wing manages to destroy her ship just before impact. At the White Moon, Lady Shatoyan, the Holy Mother of the White Moon, reveals that the White Moon is a weapons producing factory just like the Black Moon, but the people who found the White Moon decided to keep it a secret, and only use the technology there for good. Lady Shatoyan then lifts the limiters on the Emblem Frames and installs the Chrono Break Canon on the Elsior.
In the Final Battle, after defeating the Hell Hounds, Prince Eonia's elite fighter wing piloting copied Emblem Frames, Noah causes their frames to grow wings as well by altering their structure, in the process causing the fighters to consume their pilots and turn them into soulless zombies. After destroying their fighters, the Elsior gets into position and destroys Prince Eonia's flagship with the Chrono Break Canon, after which Noah reveals that Noah was just a form used to trick Prince Eonia, whom wanted to use the Lost Technology to create an age of peace and prosperity for everyone, into launching his coup so that the Black Moon could unite with the White Moon and evolve further. While the Black Moon pulls the White Moon out of orbit in an attempt to unite with it, Meyers and the Angel Wing breaks through a large screen of attack satellites to use the Chrono Break Canon on the Black Moon, but before it can finish charging, the Black Moon brings the full weight of its power on them, disabling them, all except for the Emblem Frame piloted by Meyer's chosen heroine.
Endings
The following endings assume that Transvaal remains an empire, if the player tells Prince Shiva the truth at the beginning of the game, buys him a chess set and spends time with him, it is possible to unlock the Prince Shiva subplot, and at the end of the game Prince Shiva gives up the throne and Commodore Luft is elected President of the Republic instead.
Milfeulle Sakuraba : Makes a wish to the Emblem Frame that she will give up her life as the Goddess of Luck in order to restore power to the Elsior, which destroys the Black Moon with the Chrono Break Canon. Meyers retires from the navy to lead a peaceful life with Milfeulle, whom has lost the ability to pilot Emblem Frames as well as her legendary luck(both good and bad), while Lester leads the Frontier Research Team to find remnants of Eonia's fleet and any Lost Technology like the Black Moon
Ranpha : As the Elsior starts going down in flames, Ranpha finds her resolve and destroys all the enemies, clearing a path for the Elsior which destroys the Black Moon with the Chrono Break Canon. Meyers stays in the military as head of the Frontier Research Team, and leaves with Ranpha on the Elsior, who starts redecorating the ship as their home.
Mint: The communication system goes down on the Elisor but Mint and Meyers understood each other due to their feelings. The Elisor is heavily damaged but Meyers decides to trust Mint and charge through and destroy the Black Moon with the Chrono Break Cannon while Mint destroys all the surrounding enemies with her Emblem Frame's "Flier Dance" ability. Mint decides to quit the Angel Troupe to accompany Meyers on his mission to scout the Frontier.
Forte : Destroys all the enemies in front of the Elsior, allowing it to destroy the Black Moon with the Chrono Break Canon. Meyers becomes commander of the frontier research team, and Forte becomes his new adjutant, replacing Lester.
Vanilla : Uses her Emblem Frame's nanomachines to restore full functionality to the Elsior, allowing it to destroy the Black Moon with the Chrono Break Canon. Meyers become commander of the Frontier Research Team, and Vanilla accompanies him on the Elsior, by now largely having gotten over her past and become more cheerful.