[2] The story is set on a fictional world divided in eternal conflict between the nations of Anatoray and Disith, and sky couriers Claus Valca and Lavie Head must deliver a girl named Alvis E. Hamilton, who holds the key to uniting the two factions.
Taking place two years after the events of Last Exile, the new series is set on Earth where there is a civil war with the powerful Ades Federation conquering the other nations.
The original opening and ending theme songs from Last Exile, "Cloud Age Symphony" by Shuntaro Okino and "Over The Sky" by Hitomi Kuroishi respectively, was used in episode 15.5.
While David gives the order to fight to the last ship, Claus disrupts the speaker system to read the message written by Holly expressing her wishes for her father to return home.
Meanwhile, Claus and Lavie eventually pull ahead of vanship pilots Fat Chicken and Sunny Boy to challenge defending champion Hurricane Hawk towards the final stage of the race.
Not wanting to leave Alvis alone, Claus quickly repairs his damaged vanship and drains fuel from the downed Guild Starfish, but Lavie is hesitant about the decision.
As the Silvana enters the Dragon's Fangs guided by its combat vanships, the pursuing Urbanus and two sister ships, the Martinus and the Julianus, seal the escape route behind them.
Claus learns that Tatiana comes from a noble family abandoned by the Anatoray government, during which she reached the top of her class in the military academy until she was eventually forced to discontinue her studies.
As repairs for the Silvana are completed, Alexander later confesses that he is the surviving pilot from the mission to deliver the peace proposal to Disith and the former owner of the vanship that Claus and Lavie currently fly.
After receiving a pigeon post from Prime Minister Marius Bassianus warning of the Emperor's plans on escalating the war upon taking advantage of Disith's collapse, Sophia reveals herself as the Princess of Anatoray.
Sophia arrives at Norkia to parley with Nestor and reveals to him a copy of the peace offer lost in the Grand Stream ten years earlier.
They are informed that the capture attempt of Claudia Units[Note 1] will occur on the Guild's Covenant Day, when seventeen-year-old youths pledge their allegiance to Delphine.
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.
When Alexander sees Delphine's ship above the site of the coronation ceremony, he immediately orders that it be destroyed, but second officer Arthur Campbell refuses to comply for fear of killing Sophia.
As the vanship squadron attempts to anchor cables onto Exile, the ship's defense system activates, but Dio helps complete the objective after identifying an unprotected section of the hull.
As Covenant Day arrives, Dio takes part in the Trial of Agoon to claim inheritance of the Maestro's position by participating in mortal combat against other Guild members.
Claus and Alvis rendezvous at a fueling station in the Dragon's Fangs and makes the journey to the Grand Stream, switching vanships and navigators after each checkpoint until he is reunited with Lavie.
At the Casino Royale, the last checkpoint before the Grand Stream, Claus and Alvis reunite with Lavie, who holds the message tube containing the Mysterion of House Bassianus.
As Exile enters Disith territory while continuing its indiscriminate attack, the alliance fleet loses one-quarter of its battleships, but Sophia declares to her crew that this has become a war of attrition.
The world of Prester is revealed to be in the shape of an hourglass, and Exile takes Claus, Lavie, Alvis, Tatiana, Alister, Holly, Mullin and Dunya back to Earth.
Thanks to Fam and Giselle, along with the other Sky Pirates, the Ades Federation fleet is tricked into shooting each other due to smokescreens and faked light signals, as well as fooled into believing the Lasas has sunk.
At Kartoffel, the fortress of the Sky Pirates, Millia blames Fam for failing to rescue Liliana, witnessing the Lasas being sold for scrap metal.
In their first mission, Fam, Giselle and Olaf disguise themselves as couriers for the Ades Federation and trick Ernest to leave from his outpost, allowing them to successfully commandeer the ship-of-the-line Prince of Victorius without bloodshed.
Farahnāz, Luscinia and Alauda witnessed Vasant being harassed by other Ades Federation soldiers for being chosen to present the bouquet to the winners of the race, despite her being annexed from her homeland Chaos.
Fam, Giselle and Millia arrive at a nearby Sky Pirate settlement called Spargel to refuel, but they find it bombarded and abandoned due to the work of the Ades Federation long-range auto-cannons.
Fam, Giselle and Millia visit Morvarid on a diplomatic mission to meet Vasant, who justifies that Luscinia has tyrannically betrayed the peaceful wishes of the late Farahnāz.
Fam, Giselle and Millia are informed by Dio and Alvis, upon their return to Boreas, that they managed to escape from the Extermination Squad, since Luscinia is searching for the Key to the Anatoray-Disith Exile.
However, Sadri transmits a signal to Ōrang's flagship, the Admirari, to order a pincer movement, causing mass confusion and friendly fire between the Third Fleet and the Adamas Squadron.
The Silvius timely emerges from the Grand Lake and ambushes the First Fleet, in which Sadri demolishes several of the cliffs surrounding Boreas, filling up some of the crevices and allowing his battleships to escape.
The deluxe edition of this set included a model of Tatiana's and Alister's red vanship, a short fiction on the Battle of Otranto;[Note 3] unpublished articles on the series, and illustrations by character designer Range Murata.