Introducing some of Tatsumiyajima's inhabitants, like the school going children: Kazuki, Maya, Hazama (sick in bed) and the rest of the gang. And Soshi (believed to have returned from a trip from Tokyo).

Kazuki pilots the Fafner and defeats the enemy. But the children on the island, previously oblivious, must now face the horrible reality of their situation.

Various children on the island are selected for enrollment into the service, much to the dispair of many parents. Meanwhile, Kazuki discovers someone at the basement of the base. A search plane flys in the direction of the island's location. And an enemy appears at a bad time.

Kazuki rescues the search plane against the commander's orders. Their battle does not go well. And Kazuki's disobediance results in more trouble to come.

Shouko's friends and mother express concern over her medical condition. The U.N.'s fleets makes an approach to the island to pick up the Mark Sechs that they requested but is attacked by a Festum along the way.

Two Festums have appeared, and with Kazuki preoccupied with one of them, Shouko makes a decisive decision to act. Her actions saves the island and she keeps her promises to Kazuki and her mother. But the cost for everyone is too great.

Shouko's death is received with mix reactions. Kouyou's and Sakura's performance are tested against Kazuki's Mark Elf. An island showing similarities to the Tatsumiya island is discovered, a team is assembled to investigate.

The team arrive on the island and various units set out to explore the apparently uninhabited island. Things go horribly wrong however.

Efforts to rescue Maya and Kyouhei from the island come at a great cost to Kouyou. And Kouyou's friends and family react to the great loss differently.

Hiroto Douma rebels and locks himself up in the school's broadcast room, apparently upset that his dreams of stardom may not be fulfilled.

Kazuki leaves the remote island with Yukie, taking the Fafner Mark Elf with him, arriving at a rundown city. Both Fumihiko and Kyouhei speculate about the sudden departure. After Kazuki and Yukie decide to make camp, they are then attacked by a Festum. Michio Hino and Canon Memphis, both piloting Fafners, appear and annihilate the Festum. However, the two then turn on Kazuki and disable his Fafner. Both Kazuki and Yukie is taken prisoner aboard the Neo UN fleet, having the Fafner Mark Elf in its possession. Soushi tells Maya that Kazuki wanted to escape from the island, though she disagrees with him.

Mamoru Kodate, Kenji Kondo, and Sakura Kaname are among the candidates to pilot the Fafners. Meanwhile, Kazuki and Yukie are questioning the reason of their imprisonment. As a new Festum approaches, the new pilots are soon tested to defeat it. Mamoru devises a plan, ignoring Soushi's specified orders. The three collaboratively succeed in defeating the Festum, yet they are put in confinement for acting on their own judgment. Soushi learns from Fumihiko that Kazuki denies himself daily, bypassing any assimilation. Maya realizes that Soushi has feelings for Kazuki. Michio brings Kazuki to the deck of the ship, also encountering Canon, before arriving at the Moldova base.

Mitsuhiro Bertrand says that Japan was destroyed thirty years ago when toxins were emitted from the core, which prevented citizens unable to produce offspring, marking the beginning of the attempted genocide of humanity by the Festums. When the Alvis base was founded, children were able to become immune to the Festums through gene manipulation. Hester deceptively announces of a new weapon capable of defeating Festums, having the Fafner Mark Elf displayed. Yoji Hino, who revealed he had left the island five years ago to create weapons for the Neo UN fleet, offers Kazuki to work for him as a staff member. The Grendel Type Festums invade the Moldova, prompting Kazuki to fight back.

Maya and Kyouhei go on a mission to rescue Kazuki at Moldova base. At the same time, the Neo UN fleet invades the Alvis base, trying to secure the island by taking control of the red female core, revealed to be a Coagula Type Festum, however it has left its container. Meanwhile, Yoji manages to persuade Mjolnir, the Master Type Festum which has assimilated Akane Makabe, to give the Fafner Mark Sein to Kazuki. Yukie, as well as Col. Dudley Barns, questions Fumihiko and Soushi concerning the whereabouts of the female core, but the latter two are unaware of its current location. While Kyouhei fends off the Festum in the laboratory, Yoji gives Maya the research data of the Fafner Mark Sein.

The Neo UN fleet occupies the Alvis base, however the female island core is still reported missing. Back at the Moldova base, Kazuki receives the Fafner Mark Sein from Mjolnir. Idun, another Master Type Festum, consumes Mjolnir, enraging Kazuki as he continues to fight. Both Kazuki and Idun sink into a lava pit generated by the Fafner Mark Sein. Kazuki confronts his internal conflicts about his past of when Soushi's left eye was first injured and of how the green crystals were first implanted in his body. Maya and Kyouhei witness Kazuki defeating Idun in the lava pit. Kazuki later tells Maya and Kyouhei that he is looking forward to protect the island after knowing what he is dealing with.

The Neo UN fleet, taking control of the Alvis base, is faced with a new Festum that begins to assault the island. It is shown that Seri Tatekami was with the female island core, recognized as Tsubaki Minashiro, before she returns back to the base. Chizuru later finds Tsubaki and takes her to the lighthouse. Tsubaki leads Fumihiko and Soushi into a second command center. Mamoru, Kenji, and Sakura barely put up a fight against the Festum, as they are consequently defeated. Kazuki, in the Fafner Mark Sein, arrives in time, synchronizes himself with Soushi, and eradicates the Festum using a rifle gun and then a lance sword.

Maya gives Fumihiko the research data, while Kyouhei informs that Yoki sacrificed himself to destroy the Festums in the laboratory. Tsubaki, now in the Alvis base, is revealed to be Soushi's younger sister. Michio is ordered to depart from the island, while Canon is requested to stay. Yukie docks a submarine near the island, and she activates the Fenrir System self-activation sequence. Michio becomes aware of this and warns the base of the threat. Kyouhei attempts to disarm the sequence, but Canon overrides the system. Michio takes care of the missiles launched by the fleet, while Kazuki, now released from probation, confronts Canon, managing to convince her to disarm the sequence.

Adjusting to life on the island, Michio stays with Yumiko Tomi, while Canon resides with Yoko Hazama. All the children enjoy a moment at the beach. However, Mitsuhiro visits the island, soon discovering that the results of Maya's pilot aptitude test was falsified. He takes the issue to trial and tries to claim custody of Maya. Nevertheless, he is prevented from doing so by the testimonies of other pilots about the skewing of the test data. Tsubaki verifies all the claims and admits her involvement as well. Mitsuhiro leaves the island, warning the pilots of what is to come.

Maya, after showing progress during her training session, is assigned to be a sniper with the other pilots. Both Kazuki and Fumihiko are later invited by Michio and Yumiko to eat dinner with Maya and Chizuru. A notice is sent to inform of a bone festival that will take place in the evening to honor those to have been deceased. However, a group of Rare Type Festums soon approach the island, in which all pilots engage in battle against them. Sakura is caught by one of the Festums, and Kazuki manages to save her. Moreover, when another Festum attacks Maya from above, she shoots it at point blank, achieving victory.

The preparation of the bone festival is underway. Canon and Sakura make amends for what happened during the recent alien invasion. It is seen that Koyo, in his assimilated state, is released by Tsubaki after Chizuru had froze him in the capsule. The islanders enjoy the evening at the bone festival. The following day, the pilots realize that Koyo has left the base. They barricade him in a shrine to protect him. Soushi spars with Kazuki, while Kyouhei prepares to snipe Koyo. When Canon arrives, Koyo is reminded of Shoko from her clothing, as he is brought back to normal from his assimilated state.

After the pilots relax in the bathhouse, they are told that a training camp will be conducted during the weekend. Meanwhile, Fumihiko deduces that the recent strings of alien invasions may be a diversion to a separate agenda. As the pilots later defeat eight Festums spotted coming towards the island, sunflowers and cherry blossoms spontaneously begin to bloom. During the second phase of the training camp, the pilots are given assigned cleaning duties. They each then deal with their personal feelings and fears after the training camp.

Sakura has revealed to have undergone assimilation, due to the recent alien invasion when she was caught by one of the Rare Type Festums. After the pilots defeat three Festums, they all react upon seeing Sakura hospitalized. Fumihiko confronts Tsubaki about the string of alien invasions and the island's change of weather and wildlife. The idea of integrating the Siegfried System within the Fafner Mark Sein is mentioned and discussed at the base. A new Festum appears and counters each attack of the pilots, leaving them unable to fight. Mamoru desperately attempts to immobilize the Festum, while Kazuki successfully runs the lance sword through the Festum. However, Mamoru is killed in the process.

At a Neo UN development base, Yukie is being tested to pilot the Fafner Mark Nicht, however Idun, who has taken human form, assimilates Yukie and destroys the development facility. Kazuki, Maya, and Canon are unable to bring Kenji back to the Alvis base, following Mamoru's death. Soushi, still in the Siegfried System, faces his past. Kazuki, assisted by Tsubaki, tries to save Soushi. However, Idun suddenly attacks the island and attempts to assimilate the entire base. Though Maya, Michio, and Canon intercept, they are easily defeated. Michio then activates the self-destruction sequence and attempts to ejects, but he is captured and dies in the blast. Also, Soushi disappears, along with the Siegfried System, infuriating Kazuki.

Akane, still assimilated with Mjolnir, is rejected from merging with Meir, as she proceeds to the island. Kazuki and Maya visit Kenji with Kiyomi Kaname, in which Kenji challenges Kazuki to a match. Fumihiko decides to join the Neo UN fleet in an operation to take the the core of the Festums, much to the dismay of Kyouhei. Before the deployment of the remaining pilots, Mjolnir arrives on the island, explaining Fumihiko how Akane has accepted and blessed the Festums. Mjolnir then gives them data to reduce the assimilation process and to restore people who have been assimilated. Both Koyo and Mjolnir fend off the Festums attacking the island, as the pilots prepare for departure to the final battle.

Kazuki, Maya, Kenji, and Canon, all accompanied by Kyouhei, charge straight towards the entrance of the core in order to rescue Soushi, who is revealed to be inside the core. During the operation, Tsubaki is experiencing the death process to complete the learning process for the Festums to understand life and death. Moreover, she will need to return to the core to complete this process. Kenji maps out a plan of attack, Canon confirms the battle formations, and Maya reminds that all pilots will return back to the island alive. Soushi is being controlled by Idun, who uses the Siegfried System to exploit the weaknesses of the pilots, that being to break their battle formation.