To celebrate the end of the summer break, several of Negi's students hold a pillow fight in Mahora's old elementary school building, with Negi in the middle of everything.
Negi forms a Probationary Contract with the rest of Class 2-A so they will help him fight the demons and break the contract between Asuna and the Demon King.
Kazumi starts investigating about a classmate named Sayo Aisaka, whom everybody seems to not notice she is present, not even Kazumi herself. It turns out Sayo was a student of Mahora Academy during the 1940s — and is now a ghost.
Home in the family estate for the summer break, Ayaka gets a visit, to her delight, from Negi and, to her horror, the rest of the class. Ayaka's childhood memories with Asuna are also brought up, mentioning how Asuna made Ayaka smile and laugh again after she was saddened by her little brother's death.
To help Nodoka confess her feelings to Negi, Yue gives amusement park tickets to the pair so they can have a date. Yue and Asuna follow to support the two of them.
With Konoka's safety already in danger, Negi, Asuna, and Setsuna, along with several other students, do all they can to save her.
Class 2-A finally make their trip to Kyoto, but a sinister group of mages sets its sights on Konoka.
With the help of Chao and Satomi's time machine, Negi transports himself and Chamo to 1993 Germany to know more about Asuna's magic cancelling power and discover ways to bring her back in the present. In the process, he unknowingly takes along the rest of 2-A.
Konoka causes a ruckus with Negi, in the process making a mess and breaking Asuna's alarm clock. Negi and Konoka venture to Harajuku to buy a new clock for Asuna, not knowing they are being stalked by the Cheerleaders (Misa, Sakurako, and Madoka).
Negi and the rest of Class 2-A are saddened by Asuna's death.
Negi receives a laptop computer from the Academy, but neither he nor most of the class know what to do with it. Upon Chamo's suggestion, he urges the class to help him build a homepage. The class's new site then competes against that of a net idol who turns out to be one of their own.
With his stint in Mahora on the line, Negi and the Baka Rangers (Asuna, Yue, Kaede, Kū Fei, and Makie) explore Library Island's basements for a magical book that will make his five class dunces smarter for the exams.
Negi learns ninja skills from Kaede. Upon his return, he forms a Probationary Contract with Asuna and the two set off to stalk and face Chachamaru.
Negi finally faces Evangline using his newfound skills.
Stunned by Nodoka's confession at the amusement park, Negi ponders on how to answer it. Meanwhile, inspired by Nodoka, Asuna bakes a cake for Takamichi's birthday.
Asuna is saddened when she saw Takahata together with Mahora's counselor.
Chamo arrives at Mahora Academy to personally bring a letter to Negi. But this ermine's visit is for more than an errand. Chamo's real intention was to find Negi a Pactio partner.
Evangeline starts her rampage against Negi as she victimizes several of her classmates.
On an errand towards the Tatsumiya Shrine, Negi is guided by the Narutaki twins (Walking Club).
Class 2-A battles in a dodgeball match against some high school girls who are also smitten by Negi's looks.
Stuck for three days in one of Library Island's basements, Negi and the Baka Rangers manage to escape. When Negi was about to leave the school, it turns out that 2-A got the second-highest score in the exams.
Zesu Warukiuresu corps to lead approached to castle town binon ten steadily. Rye gut believing that surprise attack is not the real intention of zesu makes a sortie for negotiations alone in derufingu. Two who met as deadhead confront younger brother of the chief secretary in battlefield in military academy after time of four years. Negotiations not to hand over when partner should retire from soldier arrive at unexpected fate before long…
While the rest of 2-A welcome Negi to their class, Asuna and Negi try to put up with one another now that she knows that Negi is a mage in training.
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.
The pilots of Tatsumiyajima are struggling more than they expected in the battle when a new power suddenly springs forth. Sui is left terrified after a brush with death, Reo is frustrated after losing in a sword battle, and Seri begins to doubt the very fact that she's alive.
Asuna starts to recall her past, seeing flames in her dream, and remembering the 10 year contract with the demon. Asuna dies.
Negotiations broke down, and battle was reopened. Both militaries were rye GATT which barely left mixed and confused confused fight, but meet with subordinate, rii of zesu. We are forced to single combat. rii which becomes rash for the loyalty and military exploit to zesu, and corners rye gut by severe attack. It was reality of too severe 〝 war 〟 that rye gut saw while movable limit of derufingu approached.
Rye GATT which did harshness of battlefield in one of eyes, and decided return once. But we know determination of hozuru which does not hesitate to conduct surrender for people either and choose way becoming soldier by oneself. Genius 〟 borukyusu general of 〝 war that begins to move in Athene's while the Krishna military gets powerful power called derufingu. And attack third wave of Creo warukiuresu corps which lost rii flocks in binon ten.
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.
"Deadhead" Rye who does not have magical power is summoned to Krishna King Hozuru and Queen Sigyn who are friend of the military academy era and is informed of fact of within the territory invasion by neighboring country Athens federation. As for the front commander being close friend, Zesu of three people. When we marched into Kodaiohei [under Gouremu] 1,000 years before estimate excavated in castle town accidentally, fate of Rye begins to greatly move…
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.
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.
Kodaiohei [under Gouremu] awakened to from sleep of 1,000 years by boarding of Rye gut crushes Quartz by overwhelming power; at last; appear. Fierce attack corps of Zesu standing in the way before confused Rye. Ex-close friends who assume fate of the mother country in the middle of intense battle, and meet again. Rye which had huge power that only he can change in its hand is swallowed without mercy to whirlpool of war.
Multiplex armor and derufingu equipped with wide end crush Aruga's machine and crush body pit of Zesu machine. Creo overwhelmed enemy force by desperate charge, and oneself became the body of prisoner although we achieved zesu rescue. Rye gut which is merely collapsed for first campaign that might kill ex-close friend. And, as boarding person of erutemisu which we requisitioned, mysterious man, jirugu is chosen….
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.
The team arrive on the island and various units set out to explore the apparently uninhabited island. Things go horribly wrong however.
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.
Three new pilots have been chosen: Mikado Reo, Kaburagi Sui, and Mikagami Mimika, third-year students at Tatsumiyajima Middle School and juniors to Kazuki and the other pilots. They have received more advanced genetic manipulation than the previous pilots, and each has unique strengths. Hazama Yuuko and Canon prepare their mechs, but the new pilots are dissatisfied with their colors and names... Meanwhile, Fumihiko and Chizuru have the difficult job of notifying the new pilots' families of their children's new placement.
June 25, 2150. One of the few surviving locations on Earth populated by humans, Hawaii, was attacked by Festums. The Neo United Nations declared ROE Alpha, burning the island and all its survivors to ashes.
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.
Festums cause chaos by attacking Srinagar, the base where the Tatsumiyajima expeditionary force is stationed, from both inside and outside. Maya runs to Yumiko and Miwa, but is shocked when she sees what Miwa looks like after trying to make contact with a Festum.
In order to initiate the regrowth of Ashoka the World Tree, the Mir fragment needed for Miwa and Altair to converse, Narain leads the Esperantos and the refugees to a new land. First they head for the Human Army base at Dhaka, accompanied by Kazuki and Soushi, but on the way they encounter a blinding sandstorm... and a swarm of enemies.
The actions of the Human Army send a shock through everyone in the camp. Wounded and desperate for salvation, everyone's true feelings begin to spill forth. Meanwhile, flight from Tatsumiyajima is still impossible and effects on the island ecosystem have grown severe. Their sights turn toward devising an escape, and Alvis depends on the Fafners' SDPs to break free of the current crisis. On top of everything, the pilots' new assimilation phenomena continue to worsen...
A giant Azazel-type Festum, called a Walker, attacks Tatsumiyajima, having been observing the island since Emery arrived there. The Walker blasts the shields open and sends Sphinx-types and other Festums inside.
A group of emigrants who strayed from the main party have been attacked by Festums. The Fafner unit, excluding Kazuki and Soushi, rush to help, but Kazuki insists that the two of them should have gone out in Sein and Nicht.
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.
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.
As the Human Army's large fleet approaches, the voice of Tatsumiyajima finally reaches them in the form of Birds sent by Fumihiko. Human Army forces begin to abandon the Neo UN's cause and aid Tatsumiyajima against the enemy core and those under its manipulation. As the battle goes on, Altair makes its appearance at last...