Sophia leaves the Silvana to return to the Anatoray capital. When General Vitellius informs the Emperor that Duke Mad-thane has engaged the Disith fleet in Norkia, Prime Minister Marius pleads with him to spare the Disith, who have recently lost their homes. However, the Emperor has already put the Disith envoy to death and places Marius under house arrest. Mullin begins to question why he remains on the Silvana, and reminisces his days as a musketeer. Alex finally considers launching a strike at the Guild, and Claus reveals to Lavie that their vanship belonged to Alex. When Sophia arrives at the capital, she also pleads with the Emperor to set aside differences with Disith and face their challenges together, but he declines and imprisons her in the tower. Sophia is visited by Marius, who raised her after his daughter Euris died in the Grand Stream, and is asked to remain in the tower until after his plans for her to become Empress is completed. That evening, Disith forces make a surprise attack on the Anatoray capital, whose defense fleet is stretched thin. In the confusion, Marius assassinates the Emperor but is fatally wounded himself. As Disith forces enter the capital, Vincent heads to the tower to prevent the Emperor's men from killing Sophia and takes her to safety on board the Urbanus, taking command of the ship again.

In the Emperor's absence, Sophia orders the Urbanus to stop General Vitellius from attacking Disith in compliance with a ceasefire. The arrival of Duke Mad-thane's fleet forces Disith to withdraw. The following day, a vanship courier arrives with a message from Walker, who invites the Silvana to Horizon Cave for repairs and resupply. Lescius reveals himself as a member of the purged House Dagobert and entrusts Alex with the third Mysterion. Prime Minister Marius, a member of the purged House Bassianus, also sent the final Mysterion to Alex before his death. The Silvana finally arrives at Horizon Cave, currently used as a training base for an assault against the Guild. Although the Guild suspects of a rebellion, Delphine decides not to take immediate action. At the base, Claus meets Mikhail Wednesday, elder brother to the late Ralph Wednesday from whom Claus took over the duty of delivering Alvis. Claus and Lavie are also reunited with fellow vanship pilots from Norkia after Duke Mad-thane, who was inspired by Claus's and Lavie's actions at Minagith, called for all pilots to fly as fighter support.

Sophia arrives at Norkia to parley with Disith commander Nestor Messina and reveals to him a copy of the peace offer lost in the Grand Stream ten years earlier. As a gesture of goodwill, Disith supplies Anatoray with a map of the Grand Stream's air currents and a recording of Exile's acoustic signature. Mullin decides to rejoin the musketeer squad and meets the female Disith musketeer, who introduces herself as Dunya Scheer. They are informed that the capture attempt of battleship Claudia units will occur on the Guild's Covenant Day, when 17-year-old youths pledge their allegiance to the Maestro. Before the Silvana leaves dock, Claus, Lavie, and Alvis say goodbye to Mullin. The formal alliance between Anatoray and Disith is signed at Sophia's coronation as Empress. Claus, Tatiana, Dio, and Lucciola arrive ahead of the Silvana to send congratulations, but Delphine's ship appears from the clouds above and rains down rose petals as a declaration of war. Dio, realizing that he has been found by his sister, panics and flies his vanship erratically. When Alex sees Delphine's ship above the site of the coronation ceremony, he immediately orders that it be destroyed, but his crew refuses to comply for fear of killing Sophia.

The Guild declares war on the new alliance during Sophia coronation ceremony, while the Sylvana heads towards an ambush.

As the Silvana and the Urbanus continue their search for Exile, Sophia briefs the vanship pilots on their strategy to capture it. Sophia asks Dio to fly as Claus's navigator, but he refuses from fear of being found again by Delphine. At Horizon Cave, Nestor proposes that the Claudia unit capture plan be accelerated after the Guild recalls several units, but Duke Mad-thane appeases him to wait for the scheduled operation on Covenant Day. On the final day of the Guild's Birth Week, Alvis surprises Dio with a birthday party, much to his delight. After days of searching, the Silvana and the Urbanus locate Exile, and Dio agrees to fly as Claus's navigator to assist in its capture. The Guild locates Dio on board the Silvana, and Delphine orders Lucciola's brother Cicada to retrieve him at all costs. As the vanship squadron attempts to anchor cables onto Exile, the ship's defense system activates, but it is able to complete their objective after identifying an unprotected section of the hull, with Dio's help. Alex hands Marius's Mysterion to Sophia and tells her to return to the Urbanus. Just before Claus and Dio return to the Silvana, Guild fighters land on the flight deck.

When Claus and Dio return to the Silvana, the crew is missing. When they go to search the bridge, they find that Delphine has captured Alvis and the ship. Tatiana and Alister sneak a transport carrying Sophia back to the Urbanus. Alex comes out of hiding to attack Delphine but is defeated by Cicada. Delphine takes Dio back to the Guild along with Claus, Alvis, and Alex, and orders that Exile be secured before they leave. On the Urbanus, Vincent promises Sophia that he will recapture the Silvana. When they return to the Guild, Dio is taken to prepare for the Rite of the Covenant. Delphine indulges in the world's rarest delicacies at dinner, causing Claus to become upset about her disregard of the hardships of the people of Anatoray and Disith. Dio is reunited with Claus and Alvis, but they find that his personality has changed and he no longer recognizes them as friends.

After the Urbanus locates the Silvana and ensures its safety, Sophia returns and is surprised that Claus has been taken. Covenant Day arrives, and Dio takes part in the Trial of Agoon to claim inheritance of the Maestro's position by participating in mortal combat against other Principals. Claus, who cannot bear to see Dio fight, worries that he may die. At the same time, the operation to capture Guild Claudia units commences at Horizon Cave. On the Silvana, Lavie finally completes the repairs of her and Claus's vanship. Delphine takes Alvis and Claus to the location of Exile, where they find its defense system has begun attacking Guild ships as well. Exile attacks Delphine's ship but stops when it senses Alvis's presence. Delphine reveals that Exile is a colony ship used by those who first settled on their world. Alex, who has been injected with a truth serum, recites the Mysteria, and Alvis responds to each one. However, he reveals that he has not read the final Mysterion before entrusting it to Sophia. Delphine then receives word that Dio is the Trial's victor.

Claus and Al escape with Luciola's help, but Dio fate is yet to be decided...

A portion of the Guild fortress breaks apart and falls away from the Grand Stream into Anatoray. Claus escapes in the vanship that was brought with them to the Guild stronghold and takes Alvis and Dio to Norkia. Dio is then left in the care of the Mad-thane residence, which has been converted into a makeshift hospital. Claus takes Alvis back to his wrecked house, where they stay overnight. The combined Anatoray and Disith alliance fleet launches a surprise attack on the Guild fleet and, helped by the vanship squadrons, emerges victorious. It continues to pursue the withdrawing Guild ships into the Grand Stream. When Claus and Alvis are finally able to contact Lavie and the Silvana with Lucciola's communicator, they are told to make a rendezvous at the Dragon's Fangs.

Exile indiscriminately attacks both the alliance and Guild as they approach the ship, forcing the alliance fleet to fall back so that they do not lose more ships. Claus rendezvous at a fueling station in the Dragon's Fangs and makes the journey to the Grand Stream, switching vanships and navigators after each leg until he is reunited with Lavie. On the way, Claus dogfights with two Guild fighters, destroying them with Tatiana as his navigator. When Exile receives a pulse signal, it begins to retreat from the Grand Stream towards Disith, followed by both fleets. At the Casino Royale, the last checkpoint before the Grand Stream, Claus and Alvis reunite with Lavie, who holds the message tube containing the final Mysterion. They fly together in Claus's and Lavie's vanship, whose body has been reinforced for the journey in the Grand Stream, but are intercepted by Dio, who has run away from the Mad-thane residence in a separate vanship.

Exile enters Disith territory, followed by the Guild and alliance fleets. The alliance fleet loses one-quarter of its ships after Exile continues its indiscriminate attack, but Sophia orders it to continue at all costs to defeat the Guild. In the Grand Stream, Dio pursues Claus's vanship and relives their race at Horizon Cave. However, when he realizes Lucciola is not with him, Dio falls into despair and is thrown off his vanship by a gust of wind. Just as the alliance fleet falters in its attack, the Urbanus leads the remaining ships in protecting the Silvana as she makes a final attack at Delphine's ship. Alex, still a prisoner of Delphine, catches her off-guard and strangles her before breaking her neck. As the Silvana destroys Delphine's ship, Wina hears Alex's final words at her listening post. Claus and Lavie finally cross the Grand Stream into Disith, completing the feat that their fathers could not achieve. There, they find the remaining alliance fleet and bring Alvis to Exile. Claus recites all four Mysteria, to which Alvis responds, and Exile sheds its defensive cocoon to reveal a starship. Inside it, Claus and Lavie find their fathers' vanship and remains. The world they have been living in is revealed to be in the shape of an hourglass, and Exile takes Claus, Lavie, and many others to a new, conflict-free world. Claus and Lavie are reunited with Dunya and Mullin, the latter of whom has recovered from his injuries. They are joined by Alvis, Tatiana, Alister, Holly Mad-thane, and several children.