When an enormous golden being attacks the peaceful Tatsumiya Island, citizens evacuate the surface to underground protective shelters. Soshi urges Kazuki to fight this horrifying adversary by piloting the Fafner Mark XI.
Aboard the Mark XI, Kazuki has a brush with death in his first battle to save the island from the Festum. Soshi tells Kazuki about the secrets of the island. Once a paradise, Tatsumiya is no longer safe from the dangers wrought on the rest of the planet.
A probe from the New United Nations has threatened to reveal Tatsumiya. As Alvis prepares to move the island to the northwest, students are drafted as new pilots and begin grueling training.
Kazuki and Soshi pursue the Festum while Alvis begins to move Tatsumiya Island. Then a New United Nations unit interferes with the plans, moving the battle directly into the island's path.
After their discovery of Tatsumiya, the leader of the New United Nations forces Makabe to hand over the Mark VI. Shoko promises Kazuki that she will protect the island as he leaves for battle. Suddenly, another Festum attacks.
As the second Festum breaks through both of the island's shields and starts to ravage Alvis' underground shelters, Shoko reacts. Determined to keep her promise to Kazuki, she boards Mark VI to save the island.
While the pilots mourn over the devastating loss of their friend, others lament her recklessness. After a combat field test, two pilots are chosen to be a part of a fleet exploring a newly-discovered island almost exactly like their own.
Troops sent to probe the new island's core fall under attack by an army of Festums. When Mizoguchi receives orders to destroy the island with him and Maya trapped underground, one Fafner must fight while the other risks an underwater rescue mission.
Koyo manages to save the two soldiers, but fate doesn't find him so fortunate. Two pilots confront Soshi over whether he is more concerned for Fafner or his friends.
Kazuki receives an answer from Soshi. Later, a student locks himself in the school broadcast room to protest the Arcadian Project after learning his aspirations to leave the island in hopes of fame are dashed.
Kazuki takes in a bird's eye view of the outside world for the first time. His refuge from the island quickly takes a turn for the worse when a Festum approaches followed by two foreign mechs--neither party showing peaceful intentions.
With Kazuki gone MIA, Kenji and Mamoru are recruited as pilots, just as a long-range firing Festum begins to attack. Mamoru boldly leads the defense with a plan that risks his own safety--but gains his commander's trust.
At the Neo U.N. underground base, Kazuki is told he has the choice to fight or save the human race without fighting. Just as they discover new data and broadcast their plan to use the Mark XI, the base falls under attack.
While Kazuki and the Human Army battle hordes of Festum, the Neo U.N. invades Tatsumiya--only to find that the island's core has vanished. Hino entrusts data on his most advanced Fafner to Maya, who has arrived to bring Kazuki back.
Someone who Kazuki thought he'd never see again returns to give him Hino's powerful Mark Sein. During battle with a massive Festum, a childhood memory of Soshi helps him realize his role in protecting Tatsumiya Island.
A flock of Pleidaes Festum begins to wreak havoc on the island. As controls in the base start to seemingly move on their own, Makabe and his crew are lead to a second control room. The Fafner are grossly overpowered, but one pilot makes a timely return.
Makabe finally has the upper hand and recovers the island from the Neo U.N., but the Human Army's Colonel leaves Canon behind with orders to destroy the island. It's up to Kazuki to defuse the detached kamikaze pilot.
Maya's father returns to discover her medical files had been falsified, preventing her from piloting Fafner. His wife and Yumiko stand trial, facing possible exile from the island--but they aren't the only ones guilty of the offense.
Maya displays impressive stability and sharp-shooting skills during her first test flight, but Soshi is reluctant to allow her to fight. But when 5 rare Festum breech the island's shield, the newest pilot gets a chance to prove her worth.
The island commemorates those who've lost their lives fighting for peace at the Bon Festival. Then, when Koyo mysteriously wakes up from his coma, his friends step in to protect him from termination.
The pilots are stronger than they've ever been. After another battle, an unexplainable phenomenon takes the island by surprise. Then, Yumiko and Michio lead a camp for the young warriors, but it's for more than just combat training.
After collapsing in the yard, Sakura is rushed to the medical ward. Makabe approaches Tsubaki to confirm that the pattern in enemy attacks and recent phenomenon shows progress in the Mir's agenda--foretelling a potentially devastating next move.
Tatsumiya suffers more casualties when a spy sabotages the Human Army's experiments with a new Fafner model and attacks the island--disrupting a critical operation to save Soshi from the Festum.
Makabe receives a message and vital data from someone who has learned to understand the enemy. The remaining four pilots prepare for Operation Azure to save Soshi, the island, and the future of humankind.
Kazuki and his fleet take off to face the North Pole Mir. With millions of lives hanging in the balance, their success in the do or die mission is imperative--if one of them is killed, everyone's chances of survival are close to nothing.
The four pilots all reunite and defeat Idun together. Meanwhile, Tsubaki struggles with her emotions at leaving to synchronize with the island core. Kazuki, with the help of Akane, manages to rescue Soushi, bearing the assimilation. As the Meir begins to make its way to the atmosphere, Maya snipes at it, preventing it from spreading all over the world. Tsubaki has become one with island, as she dissolves into thin air. Idun, barely alive in the Fafner Mark Nicht, hinders Kazuki and Soushi from leaving the battlefield, but Koyo is able to save the two. On their way to the island, Soushi vanishes because of his near assimilated state.