Knights of Sidonia

At the massive spaceship Sidonia, having exhausted his last supplies of food, Nagate Tanikaze ventures outside home to look for food when he is spotted and captured by the local security while trying to steal some rice. Believing that his life is at risk, Nagate manages to escape the hospital where he is being treated just to be apprehended by some military cadets. One of the cadets, Shizuka Hoshijiro, accompanies Nagate while he is being questioned by the police, when a man called Ochiai appears and takes him to Captain Kobayashi, the highest authority of Sidonia. Kobayashi then proposes that she becomes Nagate's guardian, with the condition that Tanikaze enters Sidonia's Guardian pilot training program, to which he accepts. He is then registered as an official cadet and introduced to the others. Through the pilot training program, Nagate learns that the Guardian pilots' main mission is to defend Sidonia against an alien hostile species known as the "Gauna". He also learns that the last time they encountered them was a hundred years ago. Shortly after becoming a cadet Nagate befriends Izana Shinatose, a genderless person whose body can adapt to procreate with either males or females, depending of the chosen partner. After failing to impress his peers at a pilot simulator for the Type 18 Guardians since the controls are different from those he trained to perfection at his former home, Nagate is called to his first sortie. Instead of piloting one of the recent Type 18 models, Nagate is entrusted with Tsugumori, a legendary Type 17 unit that belonged to a famous war hero, much to the anger of Norio Kunato, a cadet who always wanted to become its pilot and is being dispatched with him as well. Realizing that Tsugumori's controls are similar to those he is used to, Nagate's confidence is renewed. While performing a mining operation at a nearby asteroid with the others, a Gauna appears from inside it and attacks them. This is the first Gauna to appear in 100 years and is identified as Gauna 487. The episode ends with Nagate being injured and Tsugumori suffering heavy damage.

Nagate's fellow pilot Eiko Yamano is killed and absorbed by the Gauna. Nagate regains consciousness and he fights the Gauna that has now taken the shape of Yamano, despite being ordered not to since the Heavy Mass Cannon was fired from Sidonia to drive it away. Nagate skirmishes with the Gauna but having no weapons that are able to eliminate it, Nagate retreats. The shot hits the target and the Gauna is knocked back and away from Sidonia while the remaining cadets return safely home. A funeral is held for Eiko and the high command officially announces that once again, Sidonia is at war against the Gauna. Three days later, Nagate is still disturbed with what happened and barely manages to sleep or eat properly. Even though it has only been three days, his bones have healed, but he is forced to remain wearing the casts. Meanwhile, the four highest ranking veteran pilots, led by Mochikuni Akai, pay a visit to the academy. Word gets out to the cadets, and Kunato and his friends assume they are there to see him, but are shocked when Akai completely ignores them. Instead, Akai approaches Nagate, infuriating Kunato.

The veteran pilots and Yuhata Midorikawa, another cadet, inquire with Nagate about his fight with the Gauna but decide to let it for another day after realizing that he is still in recuperation. Later at night, Nagate learns that a festival known as the Gravity Festival is being held and leaves to check it out. There is also fighting competition between guardian pilots being held and despite Kunato's best efforts, he is defeated by Akai, who remains the reigning champion. Yuhata meanwhile hacks into the records of Nagate's battle against the Gauna and concludes that Akai made use of that information to improve his skills. Back at the festival, Nagate meets Shizuka and they hang out together and Izana, who was looking for him, gets flustered upon seeing them together, injuring herself when an angered Kunato bumps into her. Nagate confronts Kunato for not helping Izana and he is injured once more while fighting him. Meanwhile, Captain Kobayashi learns that the Gauna 487 had reappeared and is approaching Sidonia. Kobayashi assigns Akai's squad to deal with it. While recovering, Nagate and Izana are invited by Akai and his friends for a ride inside Sidonia's sea area before they sortie to fight the Gauna. The next day, the cadets watch Akai and his fellow squad members Momose Hinata, Aoki Kashiwade, and Izumo Midorikawa depart to confront the enemy, but the operation ends in failure as all pilots are killed by it.

After killing the members of the Akai squad, the Gauna proceeds en route of collision with Sidonia and Captain Kobayashi orders an emergency evasive maneuver by accelerating diagonally at level 5. This causes massive casualties in the ship's residential area, despite the citizens' efforts to brace themselves. As the Gauna makes a turn back to target the ship again, Kobayashi orders dozens of guardians to defend it, and sends Kunato, Shizuka, En Honoka, and Nagate to salvage one of the weapons used by the KIA squad to fight the Gauna: the Kabizashi. However, just as Nagate's team retrieves the artifact, Gauna 487 turns it's attention to them and fires a Heigus particle cannon with a Hegius accelerator that incapacitates all their units, except for Nagate's Tsugumori. Shizuka's unit goes out of control forcing her to bail out and instead of following his orders to tow the other two guardians back, Nagate grabs the Kabizashi and fights the Gauna head on, destroying it with certain ease. As the others celebrate his feat, Nagate disobeys orders once more and leaves in search for Shizuka, despite being warned that he is distancing himself from Sidonia to a point of no return.

Nagate finds Shizuka but Tsugumori runs out of energy and the pair becomes adrift in space. Meanwhile, Kobayashi is urged by Nagate's dorm manager, Lala Hiyama, to organize a search party for him, but she refuses as well. In history class it is taught that Gauna first fell to Earth in 2109 and split the Earth in two. On August 2nd, 2384 Sidonia embarks on it's journey and the last communication with another seed ship occurred on February 26th, 2691 with the Aposims. Past history of the discovery of the catalyst in the Kabizashi, the Kabi, was discovered 600 years ago by the first strike force, which included Kobayashi, Lala Hiyama, Hiroki Saito, and Ochiai. Nagate details his life underground and details how he beat his grandfather's high score at the age of six in the Type 17 training console. Nagate and Shizuka then spends over three weeks inside the derelict Tsugumori waiting for the ship to re-energize but their supplies run out faster than planned and they are put in a dire situation until 256 guardian pilots, disobeying the captain's orders, appear and rescue them.

Nagate and Shizuka return to Sidonia where they are heralded as heroes and for their services in the last battle, Nagate, Shizuka, Kunato and En Honoka are promoted to official Guardian pilots. In the occasion, Kunato apologizes to Nagate for his previous behavior towards him and Nagate meets Captain Kobayashi, with questions for her about why his grandfather raised him in the underground and why his wounds heal an accelerated rate, but the Captain only asks for him to continue with his good work. After the party, Nagate is approached by Yuhata who asks him to accompany her in a underwater ride and Shizuka and Izana accompany them. However, Yuhata attempts to get alone with Nagate in a bathysphere and when the others interfere, Nagate ends up riding alone with Shizuka instead. The two spend some quality time until they are called for another sortie, as a large Gauna pod is seen approaching Sidonia. Nagate departs to confront the Gauna 488 with Shizuka and wakes up some time later in the hospital, where he learns, to his horror, that Shizuka was killed in the battle.

After discovering Shizuka was one of the casualties during the battle, Nagate recounts the events and what ensued during the fight: Nine squads of frames (36 guards) are deployed to destroy Gauna 488 with Kunato's squad tasked to destroy the tail of the massive Gauna using explosives. Kunato, Shizuka, En and Nagate plant their explosives around the tail of the Gauna and prepare to detonate on Kunato's orders. Kunato however, activates a secure channel with Nagate and deliberately orders him to detonate the explosives too soon. This causes the Gauna to become aware of their plans and the other explosives are shaken loose due to the imbalanced explosion. All frames are then ordered to temporarily fall back and re group but Nagate loses confidence and is struck by the tail. As Nagate begins to fall unconscious, the Gauna almost kills him but Shizuka saves him at the expense of her own life. The remaining pilots do manage to destroy most of the Gauna but seven pilots are lost during the battle. En Honoka survives but is critically injured. In the present, Nagate has recovered from his injuries but is now greatly hated by the population as they believe his "failure" was the cause for the many deaths during the battle (due to the tail not being severed). Nagate takes some time away with Izana and he slowly regains his confidence in piloting the Tsugumori. Meanwhile, the captain orders the destruction of a planet, where the surviving Gauna from the previous battle have fled. With Yuhata instated as the new Executive Officer, the planet is destroyed successfully but Gauna 489, 490, & 491 appear from the planet's remains. The Captain orders Yuhata to assemble a squad (including Nagate) to intercept and destroy the Gauna. When more detailed images of the Gauna are shown, it is revealed, to everyone's shock, that the Gauna have taken the form of Guardians with the unit number 702, formerly the callsign of Shizuka.

Nakazono squad, Samari squad(units 005, 007, 026, & 174), and Kunato squad (units 701, 704, 705, & 706) confront the three Guardian-like Gauna. The Kunato squad upon after firing their Heigus particle cannon exposes a human-like ena from the Gauna. After destroying Gauna 491, Nagate retrieves a human-like Gauna sample. Samari squad engages and destroys Gauna 489. Nakazono squad engaged Gauna 490, which communicates with them through radio with Shizuka's voice after killing each squad member of the Nakazono squad. Gauna 490 continues to communicate over the radio leading Kunato to panic. The remaining Kunato squad members engages Gauna 490 resulting in the death of Ho Honoka. Upon Nagate appears the remaining Gaunua 490, later nicknamed "Benisuzume" or "Crimson Hawk Moth", retreats. After the battle, the pilots mourn five of their companions who were KIA, while Captain Kobayashi is confronted by Lala over her orders to have Nagate sortie on every mission, knowing that it may eventually lead to his death. Kobayashi then reveals that Nagate is immortal, and by not being a member of the Immortal Ship Crew that rules over Sidonia, he was seen by the other Immortals as a liability, but she claims that by having the skills of their late friend Saito, he will not die so easily. As Lala returns to the dorms, she reminisces about the events of the "Fourth Defensive War" 100 years ago when almost all citizens of Sidonia perished during a Gauna invasion. Only 392 citizens and 25 council members survived including herself, Kobayashi, Saito and Ochiai, who was held responsible for the tragedy, but was spared from execution because several important files from Sidonia's archives were copied by Ochiai to his brain while deleting the original files. The files were then relocated to an auxiliary database only accessible through his brain which was transferred to a clone of Ochiai. After the incident, Saito disappeared without a trace, only reappearing 80 years later as an old and aged man because he had renounced his immortality and refused to take life-prolonging medication. To preserve Saito's memory, Kobayashi ordered the creation of a clone of his, which was in fact Nagate, but Saito refused to have his mind transferred to the child, and kidnaps the infant Nagate with Lala's help, claiming that he will teach him his pilot skills nonetheless. Back to the present, the Gauna's placenta sample retrieved by Nagate is revealed to have the same appearance as Shizuka, and while in containment, it utters some words including Nagate's name.

The episode begins in the past, shortly after the fourth defensive war. Doctor Yure manages to integrate photosynthesizing with the remaining humans and restores Sidonia's population to 500,000 in the course of 100 years (six generations). In the present Nagate and Izana go to observe the Gauna placenta that has taken the form of Shizuka. They both meet Numi Tahiro, a scientist at Extraterrestrial Research Division (ERD), who wants to use Nagate in a series of tests to see how Placenta Shizuka would react in his presence. Nagate tries to communicate with her by mentioning Shizuka's name but it reacts violently seemingly trying to attack Nagate. Meanwhile, Kunato has relieved himself from piloting as the events during the previous battle had caused psychological distress. He then witnesses Captain Kobayashi, Dr Yure and Ochiai's clone entering an unknown area. The Captain retrieves terraforming knowledge from a site known as the auxiliary brain using the Ochiai clone, as only Ochiai's mind can enter the database, the clone is then put to sleep by the Captain's orders but she is unaware that Kunato was watching the events through security cameras. Kunato learns more about Ochiai and is interested of the "great power" Ochiai attempted to obtain. As anti-war protests continue to increase Kobayashi intends to remove them from Sidonia by allowing them to colonize and terraform the 7th planet in the Lem star system, which would move forward if 50,000 people volunteered to become colonists. As time passes both Izana and Yuhata display affection towards Nagate, but Nagate spends more time with Placenta Shizuka as it becomes less and less hostile as Nagate consistently communicates with it. Nagate is also promoted to squad leader and leads his squad on several successful battles with the Gauna, including an H-1 class Guana 492. After many battles Nagate agrees to go on a vacation with Izana to take a break. Numi analyses what Placenta Shizuka is staring at, as whenever Nagate is not present ena Shizuka would constantly stare at one point in a wall within its confined space. It is then revealed that Placenta Shizuka is actually staring at where the kabizashis are stored, far off in another part of Sidonia, seemingly scared. In the distance Benisuzume stares intently at Sidonia and at the kabizashi storage site.