Chapter 1 - スイカ畑の追憶 ネルフ日本本部急襲 - Reminiscence at a watermelon field / Sudden attack at Nerv Japan HQ Due to the actions of Ryoji Kaji, Nerv Japan HQ learned the invasion plan of Seele. In order to counter Seele's Mass Production Eva, Nerv Japan HQ pushed on with the enhancement of Unit-00 and regeneration of Unit-01. Eva Unit-02 struggled to head off the sudden attack by nine Mass Production Eva's. At this point of absolute crisis, Shinji appeared with Unit-01 Type-F. Attack in combination with Rei's Unit-00 Type-F, Shinji managed to drive them away. Geofront was invaded by one surviving MPE and the building swallowed up everyone of Nerv HQ and "froze up".

Chapter 2 - 失墜 - Downfall Nerv Japan HQ, proud of its absolute impenetrability, lost one corner of its defence - "0.0 Eva". Someone changed its architecture and, going off from Nerv HQ's control, 0.0 Eva fell onto the countryside outside Third Neo Tokyo city which was being rebuilt. Although the worst situation of S2 Engine running berserk was avoided by the actions of Shinji Ikari, it was still a big shock to everyone in Nerv. An organization that possessed the technology and know-how that could destroy a product by Nerv Japan HQ with so little effort.... For that mystery there was only one answer to that.

Chapter 3 - 黒い呼び声 - A Dark Calling Voice Shinji sortied out to meet the counterattack from Angel Carrier which suddenly made appearance. However, 0.0 Eva = Quatre unexpectedly started up without an entry plug and attacked, causing severe damage to Unit-01 Type F. Staff in Nerv tried to rescue Shinji from Unit-01 but Unit-01 stubbornly refused to budge. When as a last resort Unit-02 was called in to take apart Unit-01, a human figure with a nostalgic face appeared before Asuka.

Chapter 4 - 母から託されたもの - Thing My Mother Entrusted To Me Eva Unit-01 Type-F Modified, with Shinji merged into LCL inside, started to take off its own armor and reconstruct its body. At the same time, 0.0 Eva, which had fallen onto ground, and its pilot Rei Quatre were attacked by the Strategic Self-Defense Force and now wandered around in the mountains.

Chapter 5 - 剛き鼓動 - The Stiff Pulsation Shinji, merged inside LCL, encountered Yui, his mother whom he had lost in his childhood days. Guided by Yui, the actions taken by Shinji were...!? At that time, Unit-02 Modified had to fight Angel Carrier which came back again and attacked. Carrier's attack turned out to be much more powerful than last time and Asuka was losing. She deployed the Spear of Longinus as a weapon of last resort. However, it was taken by Angel Leliel of Another Dimension Type that was hidden in the chest of Carrier....

Chapter 6 - スーパーエヴァ出撃 - Super-Eva Sallies Forth Stuck inside LCL, Shinji encountered his mother Yui in his dream. He returned back to his childhood, talked and interacted with his mother. Receiving guiding instructions from Yui, Shinji started to mold for something. And then, apparently in response to that, Eva Unit-01 started to reconstruct itself. Not long afterwards, Angel Carrier returned to strike. Asuka and Rei, as well as all the crew in Nerv, fought desperately and frantically in the belief that Shinji would come back. Just at a hairbreadth before disaster struck, the newly shaped "Super Evangelion" appeared with a thunderous roar. Its power is so magnificent that it smashed Carrier into pieces in an instant.

Chapter 7 - 帰還 - Return Overcoming the furious battle with Angel Carrier, Shinji finally returned. Although he had had a hard time, having been scorched by Gamma Beam Laser and then melt into LCL before he was regenerated, he managed a narrow escape and survived. However, the affinity between Shinji and Eva had got overly high, and Eva followed every single step of action of Shinji. It got into motion by itself and caused issues. And then there was the sound of the "Heartbeat of Eva" coming from inside the hanger. At the same time, unusual thing was happening up in space. A black shadow appeared on the Moon at the spot where the Spear of Longinus had landed. Humanity now faced a new threat coming against them.

Chapter 8 - 黒い脅威 - The Black Threat Suddenly appeared on Mare Crisium on Moon surface was a black Evangelion. It grabbed the Spear of Longinus that had remained on Moon surface and started to send a mysterious waves of vibration to the Earth - A thumping sound that shook the ground and wore down on people's spirits. Nerv Japan HQ started up the giant mass weapon "Aten's Iron Hammer" that it had employed in space, and launched it in combination with 0.0 Eva to prepare to counter the aggression of the black Eva. Rei Ayanami on the ground lost the control of her clone, "Rei Six", inside the 0.0 Eva currently on a terrestrial orbit and she was attacked by panic. Fortunately with the back-up support from Touji she got back to stability and proceeded to intercept the Spear of Longinus. However, the all-or-nothing attack by Nerv was in vain and the Spear of Longinus was thrown aimed right at the Earth.

Chapter 9 - 宇宙（そら）を覆うもの - That Which Covered The Space (Sky) The black Eva "Armaros", which appeared on Moon surface earlier, threw the Spear of Longinus at the Earth. Neither the laser attack by 0.0 Eva, piloted by Rei Six nor the strikes by the Russian Space Forces fighters equipped with N2 warheads made any effect on it. The laser beam shots were inexplicably transformed and instead fell over the Earth like rain. All humans struck by the light were turned into salt columns. Perhaps this was a reply of the Second Impact.

Chapter 10 - 閉ざされた祈り - The Locked Prayer On the Moon surface, Eva=Armaros beat back the attack from "Aten's Iron Hammer", the biggest Mass Weapon ever built by humanity, and now stood face to face with the Earth as if mocking it. Up on the terrestrial orbit the Spear of Longinus, thrown earlier by Armaros still remained in space and lurked with its threat. Humans were scared of this threat from up in the sky. At the same time, in order to resist Armaros, Asuka and Shinji, and everyone in Nerv Japan, put in effort after effort in research and studies.

Chapter 11 - カトル来襲！ - Quatre Attacked! On the Moon surface, Eva=Armaros beat back the attack from "Aten's Iron Hammer", the biggest Mass Weapon ever built by humanity, and now stood face to face with the Earth as if mocking it. At that time, one clone of Rei Ayanami, No. Quatre, who had disappeared, showed up before Shinji. She seemed to her mind meddled by somebody and was in a confusion state - She determined that Shinji is the chief culprit for the failure of the Human Instrumentality Project and a factor of everything being led to ruin. Shinji, brought to the shore of Ashinoko Lake via space transmission, escaped the attack of 0.0 Eva.Quatre. He summoned Super Eva and counterattacked, but due to a moment of hesitation he let her slip away.

Chapter 12 - 鳥が消えた日 - The Day When Birds Disappear The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. However, this was just a sign of things to come. In order to defeat the pitch-black Eva.Armaros that threw the Spear of Longinus, Nerv Japan started to improve Eva Unit-02 so as to send it to the Moon surface. "EVA02 Allegorica" - it looked just like a Pegasus soaring up in the heavens.

Chapter 13 - 地球光 - Earth Light The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. However, this was just a sign of things to come. In order to defeat the pitch-black Eva.Armaros that threw the Spear of Longinus, Nerv Japan started to improve Eva Unit-02 so as to send it to the Moon surface. Asuka piloted "EVA02 Allegorica" in support of 0.0 Eva, which was being piloted by Rei No.Cinq, and they approached the Longinus Sphere which was located between the Moon and the Earth. The report brought in from the survey done just before the assault was shocking. The real identity of the Longinus Sphere was actually A.T.Field, which was supposed to be generated only by a living being. Did it mean the Spear of Longinus was living? The mystery deepened.

Chapter 14 - 絶滅球 - Extermination Sphere The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. However, this was just a sign of things to come. In order to defeat the pitch-black Eva.Armaros that threw the Spear of Longinus, Nerv Japan started to improve Eva Unit-02 so as to send it to the Moon surface. Asuka piloted "EVA02 Allegorica" in support of 0.0 Eva, which was being piloted by Rei No.Cinq, and they approached the Longinus Sphere which was located between the Moon and the Earth. The report brought in from the survey done just before the assault was shocking. The real identity of the Longinus Sphere was actually A.T.Field. Could A.T.Field, an impenetrable barrier, be broken through? Grave crisis was descending on humanity!!

Chapter 15 - 脅威体 - The Body Of Threat The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. Aiming to defeat the pitch-black Eva.Armaros on the Moon surface, which had thrown in the Spear of Longinus, Nerv Japan sent out Asuka and EVA02 Allegorica which she piloted. However, the real identity of the sphere that sit between the Earth and the Moon was a giant A.T.Field. Asuka was stopped at the absolute barrier. At that time the quick wit of No. Cinq, a clone of Rei Ayanami who had accompanied Asuka in 0.0 Eva, saved Asuka. By connecting with Rei Ayanami on the ground, Cinq's power was redoubled and it succeeded in neutralizing the field. It was a close shave for Asuka to escape from Longinus Sphere, but beside her Cinq's 0.0 Eva was nowhere to be seen.

Chapter 16 - 失われた切片 - The Lost Segment The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. Aiming to defeat the pitch-black Eva.Armaros on the Moon surface, which had thrown in the Spear of Longinus, Nerv Japan sent out Asuka, with her EVA02 Allegorica, and Rei No.Cinq, a clone of Rei Ayanami. In return of a tragic sacrifice, Asuka broke into the Longinus barrier surface. Just at that moment, Shinji and everyone in Nerv JPN were hit by an unforeseen situation: A white EVA02 Allegorica came flying. Who was inside? Was it Asuka who should have flown to the Moon? The situation had the alarm bell ringing loud!

Section 2 Chapter 1 - 海嘯 - Tsunami The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. Aiming to defeat the pitch-black Eva.Armaros on the Moon surface, which had thrown in the Spear of Longinus, Nerv Japan sent out Asuka, with her EVA02 Allegorica, and Rei No.Cinq, a clone of Rei Ayanami. In return of a tragic sacrifice, Asuka broke into the Longinus barrier surface. Just at that moment, Shinji and everyone in Nerv JPN were hit by an unforeseen situation: A white Unit-02 came flying. The pilot inside was actually Shinji's classmate Hikari Horaki. Shinji and Touji were perplexed. What happened to Hikari!?

Section 2 Chapter 2 - 最後のゼーレ - The Last Seele The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. Aiming to defeat the pitch-black Eva.Armaros on the Moon surface, which had thrown in the Spear of Longinus, Nerv Japan sent out Asuka with EVA02 Allegorica. At that time, an unforeseen situation hit Nerv JPN: The attack by the white Unit-02 = Eva Euro II, and then at the worst timing possible the resurrected Seele in the form of yorishiro (possessed) Kaji Ryouji. One shock quickly after another shook Nerv!!

Section 2 Chapter 3 - 歪められた庭園 - The Distorted Garden The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. Aiming to defeat the pitch-black Eva.Armaros on the Moon surface, which had thrown in the Spear of Longinus, Nerv Japan sent out Asuka with EVA02 Allegorica. Greeting Asuka on the unsightly rugged terrain on the Moon surface was her sworn enemy Angel Carrier. The guns for a rematch were to be opened up.

Section 2 Chapter 4 - 抗う者 - Those Who Fought The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. Aiming to defeat the pitch-black Eva.Armaros on the Moon surface, which, had thrown in the Spear of Longinus, Nerv Japan sent out Asuka with EVA02 Allegorica. Greeting Asuka on the unsightly rugged terrain on the Moon surface was her sworn enemy Angel Carrier. After a furious battle, Asuka, victorious, recovered her balance and started the search for Armaros.

Section 2 Chapter 5 - 渦巻く天極 - The Whirling Celestial Poles The Spear of Longinus, orbiting around the Earth, had brought the worst consequence to humanity. The Longinus Sphere, generated by the Spear of Longinus, had begun to cause the Earth itself to compress and collapse. The collapse of the tectonic plates caused huge earthquakes to strike the land and many human lives to be lost. Aiming to defeat the pitch-black Eva.Armaros on the Moon surface, which, had thrown in the Spear of Longinus, Nerv Japan sent out Asuka with EVA02 Allegorica. And then, as the trump card, the mobility refixing of Super Eva was started and it was equipped with the Vortex device that could cope with the airborne combat ability of the enemy. Just when the mobility test was finally to begin, 3 pieces of the Flying Type Angel Carrier appeared! Over the big sky the giant at least got to spread the wings!

Section 2 Chapter 6 - 黒い思惟 - The Dark Contemplation After Commander Misato Katsuragi got abducted by Quatre, Nerv Japan fell into deep chaos. Touji invited Fuyutsuki, who had been a pivotal person in the founding of the old Nerv and even now was still widely revered as the pillar of the spirits of everyone in Nerv, to join as a consultant. Also, the strong desire to equip Super Eva with the Vortex device had finally come true. Though still having wounds all over it, Nerv was finishing its preparation for the counterattack.

Section 2 Chapter 7 - Somewhere in Time In faraway Cyprus 0.0 Eva Quatre showed up. Misato finally met Kaji again. Kaji, as the successor of Seele, talked about the secrets of Seele and Human Instrumentality Project. Victor, the pair of giants released by Armaros, appeared in Japan. Super Eva charged into the dimensional window created by Victor. The furious battle continued.

Section 2 Chapter 8 - 箱船 - The Ark Misato, previously abducted by Ayanami No. Quatre, was now in front of Kaji. Kaji had been transformed into Seele's successor after his mind was overwritten with Kiel's memory. And then Misato and others were guided by Kaji to the "Valley of Humanity" which was the place where the prehistoric Eva came to die. At that time, Shinji was about to start the journey to look for Asuka who had lost contact on the Moon. Asuka's destination was the Moon surface which was supposed to be the hiding place of Armaros. Shinji jumped into the "window", a space for instantaneous movement created by Armaros. Where would the journeys of Shinji and Misato lead to?

Section 2 Chapter 9 - 閉ざされた環の中で - Within the Locked Ring Misato, previously abducted by Ayanami No. Quatre, was now in front of Kaji. Kaji had been transformed into Seele's successor after his mind was overwritten with Kiel's memory. What was Kaji trying to achieve at the "Valley of Humanity" which was the place where the prehistoric Eva came to die? And then the "Ark", the key to Human Instrumentality Project, appeared. The story of ANIMA is about to reach a roller.

Section 2 Chapter 10 - 黒と紫 - Black and Purple Misato, previously abducted by Ayanami No. Quatre, met Ryouji Kaji, who had been reborn as Kiel, again. At the same time, a number of Evangelions came down to the "Valley of Human Body", a place that seemed to be the remains of a Human Instrumentality Project back in prehistoric times, like they were all attracted by it. There were 4 altogether: 0.0 Eva Quatre, Euro II Heurtebize, Super Evangelion and Armaros which finally landed on Earth. Armaros and Super Eva finally got down to a furious fight. However, facing the overwhelming power from Armaros Shinji had to beat a retreat in defeat. The body was penetrated by the Spear of Longinus brought forward by Armaros and its heart, previously transformed from the S2 engine, was taken away.

Section 2 Chapter 11 - 弐号機の呼び声 - The Calling Voice of Unit-02 The battle at the "Valley of Human Body", the ancient battlefield of Eva, had ended. Super Eva, beaten by Armaros' powerful strength, had its heart, its source of power, gouged out and taken away. It then fell down on the ground. At that moment, Euro II started an unexpected action: It entrusted its power plant, the QR Signum, to Super Eva. As Shinji escaped from near-death status, a figure of red giant appeared before him. Its face was a mingle of human and Eva, and had the look of Asuka who had lost contact on the Moon.

Section 2 Chapter 12 - チルドレン - Children Shinji lost the battle against Armaros at the Valley of Human Body. Super Eva had its "heart", the power engine that formed its basis structure, taken away, but thanks to the quick wit of Hikari it had QR Signum installed instead, and it barely escaped from coming to a standstill. But problem did not stop here: Asuka, who made it away from the Moon through a subspace tunnel, was fused with Unit-02 and became a gigantic Eva=Human Synthesis Body.

Section 2 Chapter 13 - 道標なき旅 - Journey Without Signpost Shinji lost the battle against Armaros at the Valley of Human Body. Super Eva had its "heart", the power engine that formed its basis structure, taken away, but thanks to the quick wit of Hikari it had QR Signum installed instead, and it barely escaped from coming to a standstill. With on-location repair it was finally restarted again and began cruising towards Japan. However, Quatre, also inside Super Eva as passenger, went berserk and displaced Super Eva to another location. And the unexpected person who was waiting for Shinji's group at this strange land was....!?

Section 2 Chapter 14 - リンゴの芯 - Apple's Core Somehow after on-location apparatus modification work and emergency operation done on Super Eva to convert it to be compatible with QR Signum, it was to be transferred urgently to Nerv JPN. However, Super Eva was displaced into an unknown world by Ayanami No. Quatre who was also in Super Eva. And the person who was waiting for them there was Kaji, whose mind consumed by Seele. 0.0 Eva Quatre, controlled by Kaji, and the Angel Carrier with Angel Leliel residing in it, which once robbed Longinus from Asuka, were standing in Shinji's way.

Section 2 Chapter 15 - 対称座標 - Symmetric Coordinates Somehow after on-location apparatus modification work and emergency operation done on Super Eva to convert it to be compatible with QR Signum, it was to be transferred urgently to Nerv JPN. However, Super Eva was displaced into an unknown world by Ayanami No. Quartre who was also in Super Eva. And the person who was waiting for them there was Kaji, whose mind consumed by Seele. 0.0 Eva Quatre, controlled by Kaji, and the Angel Carrier with Angel Leliel residing in it, which once robbed Longinus from Asuka, were standing in Shinji's way. Utilizing the newly equipped Kesara Sword, Shinji was able to win. Following the guidance from Quatre, he began his return trip.

Section 2 Chapter 16 - 北の地への招待 - Invitation to the Northern Land The forces from human side that were being assembled was attacked suddenly by Victor = Taubert and suffered grave damages. Only Hikari's Eva Heurtebize managed to hold off the attack and barely prevented the defence line from collapsing. And strangest of all, the "heart" that had been taken away from Super Eva could be seen shining at the chest of Eva Taubert, a Eva that had a single black wing.

Section 2 Chapter 17 - 招待客たち - The Invited Guests Super Eva was defeated. Humans combined their last fighting forces and prepared the counterattack against Armaros. However, Taubert appeared at the assembly site and threw human forces into big chaos. Hikari and Mari were about to counterattack with Eva but before they could do that Asuka-Eva Synthesis Body appeared with 7 Angel Carriers in tow. How would Hikari confront the absolute difference in combat strength!? Also, had Asuka really switched to enemy's side? The mystery deepened.

Section 2 Chapter 18 - 行き違うエレメント - Elements Crossing Each Other Nine Eva's descended in front of the Euro-Russia combined forces. Strange phenomena were found in Taubert at the center of the Eva's. First it was installed with the heart torn away from Super Eva. Then the female-looking Taubert, which seemed to be nestling close to it, had the face of Asuka on it. The gap of combat strength was too obvious, but with smart fighting by the combo of Hikari and Mari Taubert was severely damaged and it had to withdraw from the battlefield together with Asuka = Taubert. Shinji and his Super Eva came back from the alien world just a bit too late and thus missed meeting Asuka.

Section 2 Chapter 19 - 我及ぶ限りの世界で - In A World To The Best of Myself Nine Eva's descended in front of the Euro-Russia combined forces. Strange phenomena were found in Taubert at the center of the Eva's. First it was installed with the heart torn away from Super Eva. Then the female-looking Taubert, which seemed to be nestling close to it, had the face of Asuka on it. The gap of combat strength was too obvious, but with smart fighting by the combo of Hikari and Mari Taubert was severely damaged and it had to withdraw from the battlefield together with Asuka = Taubert. Shinji and his Super Eva came back from the alien world just a bit too late and he started his battle against the Angel Carriers, his sworn enemies.

Section 2 Chapter 20 - 万華鏡の空 - The Kaleidoscope Sky The Angel Carriers was about to wipe out the Euro-Russia combined forces when Shinji came and defeated them. However, Super Eva's heart that was taken from him earlier, as well as Asuka Eva Synthesis Body, had disappeared into the void together with Taubert. After a long journey coming to an end, Shinji returned to Nerv.