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.

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.

Fam and Giselle begin their dangerous quest of capturing fifteen Federation ships. Meanwhile, Princess Millia comes up with an unexpected way to re-establish the Turan kingdom.

Claus and Lavie decide to assist in defending the Sylvana from the Guild, but do they stand a chance in this fierce battle in the sky?

Alex announces that they are going to battle against Urbanus. Although she hesitates at first, Sophie announces their mission over the loudspeakers. Meanwhile, Al has come out of her ""coma"" but she has no recollection of what has just happened. Dio refers to her as ""genuine"" but does not elaborate. Later, when Sophia confronts Alex, he tells her she can just leave the ship, but he refuses, reminding him that she is his first officer. Tatiana briefs the vanship pilots on tactics against the Urbanus, and much to Alistia's chagrin, chooses Claus to be her navi. Lavi and Al prepare water and a lunch for Claus before he takes off. Alex is leading the Urbanus, and three other ships, into the Dragon Fang. While Vincent does anticipate Alex's moves, he doesn't anticipate the other captain's desperate battle response. Despite the Urbanus dealing a crippling blow to the Sylvana, Alex is able to sink two of the Urbanus-class ships. Al and Lavi are thrown to the ground, and Lavi is knocked unco

Claus reports to Alex that Disith has become uninhabitable and that he and Lavie can no longer return home to Norkia. Rumors circulate throughout the ship about Claus and Tatiana, making Lavie upset and unwilling to speak to Claus. However, Claus does not seem to understand her actions and wants her to come to better terms with Tatiana. Alister warns Tatiana not to read too much into Claus's care for her when they were in the desert. Meanwhile, Vincent is stripped of his command of the Urbanus after losing four battleships against the Silvana and is assigned to the fleet defending Norkia. The Emperor of Anatoray decides to take advantage of Disith's collapse and plans on escalating the war, to Prime Minister Marius's objections. When Marius learns that the Silvana has completed its repairs, he decides to keep the news from the Emperor. Dio reveals a photo of Claus's and Lavie's fathers in Alex's possession, prompting Claus to confront the captain. Alex confesses that he is the surviving pilot from the mission to deliver the peace proposal to Disith and the former owner of the vanship Claus and Lavie are flying. He recounts how his fiancée, Euris, and Claus's and Lavie's fathers died and the memory of seeing Delphine smiling when he flew away from the Grand Stream. Alex tells Claus that he is fighting to destroy Exile, which reinforces the Guild's authority in the world. After receiving a pigeon post from Marius warning of the Emperor's actions, Sophia reveals herself as the Princess of Anatoray. Conflicted between her responsibility to the throne and her desire to stay aboard the Silvana, Sophia is comforted by Claus. She suddenly kisses Claus as gratitude.

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.

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.

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 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.

In the skies above the sacred Grand Lake, the Ades Federation declares war on the kingdom of Turan. Just when the Turan flagship's destruction seems inevitable, a Sky Pirate named Fam boldly states, "I’ve made up my mind! I’m going to steal that ship!"

Much to Fam and friends' elation, Turan and Anatoray form an alliance with Millia and Vincent acting as delegates. Suddenly the Impetus, an Ades Federation flagship, appears... along with Luscinia and Liliana.

The Sylvana lands for refueling and supplies, when they are faced with potential brawl with the crew of the Goliath!

Claus and Lavie progress in the endurance race, but Dio and Lucciola continue to challenge them. Duke Henry Knowles raises the bid price on the Exile artifact, spurring interest among the other auction participants. As Alex attempts to outbid the others, Guild Maestro Delphine Eraclea challenges him and finally raises the bid price to 50 billion Claudia, at which point one of Knowles's men puts a gun at the back of Alex's head, threatening him not to continue bidding. On their final pit stop, Tatiana and Alister pick up a cargo of explosive charges for their mission. When the auction ends, Duke Knowles takes Alex outside and reveals that he wants to avenge the death of his son, captain of the Goliath. Claus and Lavie pull ahead of Dio and Lucciola in the final lap after only filling part of their fuel tank at the last pit stop to lighten the vanship and win the race. At precisely midnight, the explosive charges dropped by Tatiana and Alister destroy Horizon Cave's power generators, leaving it in darkness. Seizing the opportunity, Alex kills Knowles's men and escapes. When the artifact is taken to Delphine, it is discovered to be fake. The true artifact of Exile is revealed to be a Mysterion, one of four phrases with corresponding answers that will reveal the secret of Exile. Graf, the butler of House Hamilton, entrusts Alvis and the Mysterion to Alex. After the race, Lavie tells Claus that she does not want to fly in a fighter vanship but will continue to serve as his mechanic. Claus understands her decision and makes a promise that they will fly together again to cross the Grand Stream. Dio and Lucciola, who are able to see in the darkness, offer to tow Claus and Lavie out of Horizon Cave to the Silvana.

With only one ship left until their agreement with Tatiana is fulfilled, Fam and company aim to capture a fleet of eight ships being transported from the north.

When Fam and her friends make an emergency landing in the northern nation of Glacies, they're met by a girl named Dyan.

The Winged Priestesses, led by Dyan, engage the Ades Federation armada in battle as it begins to invade Glacies.

Moran is "officially" accepted by the crew of the Sylvana, albeit in a most interesting manner. Sophia presents the chance for Claus and Lavi to enter the 8-Hour Endurance Race at Horizon Cave. They accept the challenge, so long as the Sylvana mechanics will help them out. At the event, Al is allowed to "pick" the vanship that they must repair and fly for the race. Tatiana and Alistia, however, have a mission during the race. They need to hit a specific point in the race at a specific time. Tatiana expresses her dislike of "amateurs" i.e.: Claus and Lavi, but Alex shuts her up. Dio and Luciora show up, because Dio is with his sister, Daphne. Dio shows an interest in Claus, who doesn't return the fascination. Dio informs Claus that he is there to fly in the race with him. While the race is going on, Alex is at an auction to purchase something rare. It turns out to be an EXILE item, and Alex's opening bid on it, is 10,000,000 Claudia. This shocks the man sitting next to him, who just

Following Claus and Lavie aboard the Silvana, Dio and Lucciola allow themselves to be captured. At the Anatoray capital, the Emperor begins to distrust Alex's actions and sends the Urbanus to retrieve Alvis. Alex interrogates Dio, who tries to gain his trust by telling him that the Mysterion passed by House Eraclea. He also reveals that the three Guild houses holding the remaining Mysteria have been purged by Delphine. Vincent Alzey, captain of the Urbanus, requests to meet with Alex. Alex asks Claus to fly escort for his flight to the meeting, to which Tatiana objects. Alister defies Tatiana and offers to be Claus's navigator. Alex informs Vincent that he will not hand over Alvis and will fight to keep her aboard. Dio and Lucciola meet Lescius, the Silvana's chief engineer and a former member of the Guild. Dio then finds Alvis by herself elsewhere and reads her one of the Mysteria, after which she falls into a trance and wreaks havoc on the ship's systems.

Princess Liliana is sent to Iglasia with instructions for defending the royal city from the Federation assault. Meanwhile, Princess Millia readies a surprise attack of her own, but little does she know Luscinia has a trick up his sleeve too...

With her kingdom now under Federation control, Princess Millia finally begins to understand what it means to be a Sky Pirate. Fam also reveals details about her past and her dream for the future.