In an attempt to gather information on immortality, scientists from around the world have assembled to study Heaven's Gate—the tomb turned laboratory of the mythical king Gilgamesh. But soon enough, the research is deemed unethical and all planned work comes to a halt. However, a group of terrorists pay this no thought and storm into Heaven's Gate, ultimately causing an explosion that leads to the collapse of the advanced information civilization. Many years after the incident, the siblings Tatsuya and Kiyoko Madoka are on the run from thugs. Yet this seems to be the least of their worries as they find themselves in the midst of a war between two powerful cryptic factions. With both groups claiming to fight for the betterment of society, Tatsuya and Kiyoko will have to find a way to decide who to trust.

Led by Reinhard von Müsel, the Galactic Empire crushes the Free Planets Alliance in the Fourth Battle of Tiamat. Arriving in the Imperial capital of Odin to a hero's welcome, Reinhard's victory earns him a promotion to High Admiral and the distinguished title of Count von Lohengramm. On the other side, Yang Wen-li safely returns to the Alliance capital of Heinessen without fanfare and reunites with his dear friends. Reinhard and Yang look forward to a long-awaited reprieve. However, at the request of the scheming Duke Otho von Braunschweig, the Imperial High Command orders the new High Admiral to invade the Alliance with a fleet of twenty thousand ships. After the Duke leaks the plan to the Alliance government, three fleets totalling forty thousand ships are sent to counter the incoming attack and recreate the famous Battle of Dagon. But even though Reinhard is outnumbered two to one, he has an ingenious plan—and Yang sees right through it. Will Yang's superiors heed his warning before it is too late?

Marquis Reinhard von Lohengramm's plot to destabilize the Free Planets Alliance succeeds when the treacherous former Rear Admiral Arthur Lynch instigates a coup on Heinessen. Equipped with a plan crafted by Reinhard himself, Lynch encourages his longtime friend Admiral Dwight Greenhill to supervise the National Salvation Military Council's toppling of the civilian government. Seeking to defend democracy and restore the Alliance constitution, Admiral Yang Wen-li faces off against his fellow citizens—and, regrettably, the father of his devoted adjutant Lieutenant Frederica Greenhill. Now with the Free Planets Alliance thoroughly occupied with their own internal matters, the forces of the Galactic Empire can safely suppress the newly formed Lippstadt League led by Duke Otto von Braunschweig. However, with his friend and loyal subordinate High Admiral Siegfried Kircheis fighting far away in the noble-controlled frontier regions, Reinhard increasingly relies on the advice of the ruthless Vice Admiral Paul von Oberstein, whose influence within the esteemed Lohengramm admiralty steadily grows. Though bloodshed is inevitable on both sides of the galaxy, Yang Wen-li of the Alliance and Reinhard von Lohengramm of the Empire each ask themselves the same questions: how will history look back on their actions? Will the ends justify the means?

The red-light district, Yoshiwara, is suddenly taken over by Aizen Kou, an incense that has the ability to make anyone fall in love with the first person they see. Having been outlawed for its strong potency, the love drug was thought to have disappeared from the red-light district for good; however, it seems to have found its way back inside Yoshiwara's walls and now has the entire district under its influence. Of those affected is the cold-hearted Hyakka captain, Tsukuyo, and the first person she sees after inhaling the smoke is none other than the brazen Yorozuya leader, Gintoki Sakata. Unbeknownst to everyone else though, she was already attracted to Gintoki. With those hidden feelings now intensified, Tsukuyo must overcome her afflictions and work with the Yorozuya to return everyone back to normal.