Fam and friends return to Kartoffel after their long absence. The joy of seeing everyone safe and sound again turns to shock as Fam sees what has happened to the town.

Millia and friends have an audience with Augusta Sārā in the capital city of Morvarid.

The Ades Federation’s 3rd and 4th Fleets advance on the key strategic land of Boreas. A decisive, multi-fleet battle over Augusta Sārā ensues. Millia takes command of her fleet, while Fam and the Sky Pirates take to the air in armed Vespas.

Dio and Alvis meet up with the Joint Forces at Boreas and lend a big helping hand. But their joy is interrupted when Fam's group spots Ades' 1st Fleet while on patrol.

Upon hearing Sārā's wish, Admiral Sadri agrees to peace. A meeting takes place between Luscinia, Liliana, Sārā, Millia, Vasant, and others.

The truce has fallen apart. Before leaving, Luscinia tells Fam, "Be there to support Princess Millia."

After abducting Augusta Sārā, Luscinia activates the Grand Exile.

Fam and Giselle reach the furthest depths of the Grand Exile. There, they find Luscinia, holding a sleeping Sārā.

Claus and Lavi are back at their home, with Alvis sleeping on their bed. Claus has decided to take the mission, much to Lavi's annoyance. Alvis awakes and asks for her nanny, Gita but the woman died during their escape. Claus isn't sure how to handle it, but Lavi tells Al that Gita had to go away for a while. After eating, they settle in for the night, but the star-shaped ship finds Al in the house. Claus and Lavi have to escape, and their house is destroyed in the process. Although they don't use their engines in the waterway, the star-shaped ship still finds them. They narrowly escape, appearing to damage the star-shaped ship enough to do so. At the temple ruins, where they were to bring Al, they are attacked again and the star-shaped ship snatches Al. Claus tries to fight it with a rock and is knocked out. Just as he is about to be killed, a shot rings out. Alex has shot the pilot of the machine and saved all the children.

Alex kills the pilot of the star-shaped ship and takes Alvis on board the Sylvana, leaving Lavi and Claus behind. Claus repairs the vanship and obtains extra fuel from the downed ship nearby. He and Lavi then follow the trail of the Sylvana, for Al's sake. Al wakes up on the ship and meets Sophia. When the vanship catches up to the Sylvana, Alex allows the ship to fire upon them, but they are able to avoid getting hit and they ""crash-land"" on the Sylvana. They encounter mechanics in the hanger, and Claus is beaten up by one of them for fun. However, Tatiana and Alistia show up and Tatiana grudgingly asks for Claus' name. Lavi helps Claus up to the bridge, where they meet up with Alex again. At that point, Claus' injuries get the better of him, and he falls unconscious.

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

While Lavie recovers from her injuries on the crashed Silvana, she dreams of her childhood with Claus, whose family moved to Norkia and became neighbors with Lavie's. Their fathers, Hamilcar Valca and Georges Head, immediately became best friends and teamed up as a vanship pilot and navigator. Claus's mother, Justina, took care of Lavie as if she was her own daughter. Valca and Head taught their children to fly a vanship and assigned them mock courier missions. Lavie recalls her father's two friends, a male vanship pilot and a female navigator, but cannot remember their names. One day, Valca and Head received an assignment to cross the Grand Stream to deliver a peace proposal to Disith and left with their two friends. However, Valca and Head lost their lives in the attempt, and Justina died not long after. In a separate dream, Alex Row sees the two vanships in the Grand Stream. After they were orphaned, Claus and Lavie began training to fly a vanship. They were eventually forced to sell their house to save the vanship and began training for courier missions. When Lavie finally awakens, she finds herself crying from the memories. Dio and Alister finally locate Claus and Tatiana near the field of Disith migration capsules. Claus is reunited with Lavie and informs her that their hometown of Norkia has fallen to Disith.

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.

Ten years ago, the first Grand Race was held. A young Fam and Giselle cheer on Atamora as he competes in the championship race.

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...

To help Millia rebuild Turan, Fam decides to steal a legendary ghost ship known as Sylvius the Reaper, a ship that is said to have single-handedly destroyed an entire Ades Federation fleet. With so few details to work with, though, it won't be easy.

In the hope of capturing their next battleship, Fam and company visit Eldorado, an amusement center where underground Vanship races are held.

The final target was the Anshar, the flagship of the Ades Federation's 1st Fleet. Now that their agreement with Tatiana has been fulfilled, Giselle prepares to leave the Silvius... but without Fam.

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.

The Silvius finds itself face-to-face with the Ades Federation's 1st Fleet, which had been silently tailing Fam and Giselle.

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.

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.

Just as Claus and Lavi deliver their message to Duke Madossein, The Guild is hit. Duke Madossein instructs everyone to get to safety, and Claus and Lavi are escorted to their vanship. However, just as they are about to leave, Claus remembers he still has his letter from Holy. Lavi rigs the PA system in order to read it to the Duke and everyone else on board. However, this could be cut short as the first officer send guard to stop Claus and Lavi. But the guards aren't the only ones heading for Claus and Lavi, as Mullin Shetland is touched by the words from the letter.