One of Nagate's fellow pilot trainees at the series' beginning and a person of the third gender. One of the first people to befriend Nagate and treat him as a fellow human being, Izana proves to be his closest friend as the series progresses, and a source of great moral support. Izana quickly develops feelings for Nagate, which go mostly unnoticed due to his lack of social awareness.
Izana eventually becomes a regular pilot and loses an arm and a leg at the hands of Benisuzume, but obtains mechanical limbs to compensate.

An Arm and a Leg: On Izana's first mission as a regular pilot, her right arm and left leg are destroyed by Benisuzume.

Artificial Limbs/Badass Transplant/Swiss Army Appendage: Izana's artificial right arm. It grants her enhanced strength, fingers which can split and extend and a Brain–Computer Interface.

Cowardly Lion: At the beginning of her pilot career.

Custom Uniform of Sexy: Izana gets later a very distinct skintight, half-black pilot suit.

Cute Clumsy Girl: A trait Izana inherited from her grandmother.

Cyborg Helmsman: Of an old, armed Sidonian cargo ship during the Teruru rescue mission.

Does Not Know His Own Strength: Nagate is comically injured several times because Izana was not used to the superhuman strength of her new right arm.

Gender Bender: 3rd Genders like Izana start off asexual, but will become either male or female after choosing a mate. hence, she starts turning female after developing feelings for Nagate.
Hermaphrodite: The series' first and most focused on example.

Everybody Wants the Hermaphrodite: Heartbreakingly averted. Izana loves Tanikaze deeply but he only likes women (and is incredibly dense, to boot).

However, Izana eventually transforms into a female. This is because Third-Gender's like Izana aren't really "Hermaphrodites" per say; they're asexual humans who don't have a set gender, but have the ability to become Male or Female later in life. The transformation is triggered when, consciously or not, they decide on a mate, and Izana's began after she fell in love with Nagate.

Izana is later voted the most popular person on board the Mizuki among both men and women. By that point in time Izana has fully become a woman, however, making this a subversion of sorts.

Identical Granddaughter: Yure remarks that after her transformation into a girl Izana looks like her when she was young.

The Lancer: Becomes one in the course of the story to Nagate's Hero.

Locked Out of the Loop: Izana's grandmother keeps her in the dark about her real work and true standing in Sidonia. It lasts till chapter 65.

Nice Gal/Guy: It's established in her first appearance that he's got a very calm and sweet disposition. However...

OOC Is Serious Business: S/he becomes a little temperamental in later chapters, prone to pouting and and very Tsundere-ish outbursts. It's a hint that Izana's body is undergoing stressful changes.

Raised by Grandparents: Raised by her grandmother Yure Shinatose.

Slow Transformation: Izana's gradual transformation into a female takes more than thirty-three chapters. It also embarrasses the hell out of her.

Super Senses: She can receive and process data from Sidonian sensors via her Brain–Computer Interface. Her sensor radius amplification device amplifies them with help of other Guardians and drones to the point that they surpass the senses of chimeras, the most advanced individuals of the setting.

Sensory Overload: She has to keep her eyes closed when she processes data from sensors in order to prevent an overload.

Wetware CPU: Izana's brain is used to process data from various Sidonian sensors into visual and auditory output.

The second-ranked trainee in Nagate's class at the start of the series, Hoshijiro is Nagate's main Love Interest, being the first woman he ever saw and felt romantic affection for. Following the battle with the Gauna mimicking Yamano Eiko and being rescued by Nagate, she reciprocates his feelings.
This turns out to be a rather brief relationship, as in their next mission Hoshijiro is killed saving Nagate and assimilated by a Gauna, her memories and DNA used for creating a trio of powerful Guardian-type Gauna codenamed "Benisuzume" (Hawk Moth). Gauna 489 and 491 are killed in their first sortie, but Gauna 490 - implied to be the same Gauna that assimilated Shizuka - escapes and becomes a reoccurring antagonist. A placenta sample of Gauna 491 is retrieved by Nagate, and is eventually used by Ochiai to give birth to Tsumugi and later Kanata. However, a second placenta sample was retrieved from Gauna 490, and has not been altered in any way.
And Then Hoshijiro Was A Gauna: She's assimilated early in the manga and three copies of her show up as powerful antagonists.
Attack Hello: Once put in containment, the first placenta's first response to seeing Nagate was to launch a flurry of tendrils at him.
Body Horror: Hoshijiro finds out first hand what Gauna do to their victims, and they use a corrupted parody of her body as a placenta for Benisizume.
After being impregnated by Ochiai, 491's placenta-copy's body undergoes grotesque transformations during Tsumugi's gestation.
Breath Weapon: The Guardian portion of its body can spit crimson Higgs beams.
Cute Monster Girl: The first Hoshijiro placenta's interactions with Nagate were adorable.
Energy Absorption: Gauna 490 drained Tsumugi's Higgs particle supply during their fight, and would have killed her if Nagate hadn't intervened.
Evil Uncle: Gender-flipped: Gauna 490 nearly killed Tsumugi, who is Gauna 491's - for all intents and purposes 490's twin sister - daughter.
Expendable Clone: There were three Benisuzume, dubbed Gauna 489 through 491. 489 and 491 are killed in the first confrontation, but the one named Gauna 490 by humans escapes and evolves over the course of the series, with its last and strongest appearance resembling a skeletal version of Shizuka with wings.
Exotic Eye Designs: Gauna 490 has red eyes with a grid-like array of white pupils.
Fangs Are Evil: Gauna 490's helmet has a fanged mouth on it.
First Girl Wins: She's the first girl Nagate sees, and she and Nagate fall in love with one another. Even after her death, she ends up having much relevance in the series, as Nagate is shown to still miss her even dozens of chapters after her death, and her copies appear to retain some degree of affection towards him.
Giggling Villain: Gauna 490 seemed to find killing its former comrades amusing, since it was laughing throughout its first sortie.
Good Colors, Evil Colors: The Guardians are robotic and white, while Benisuzume is biomechanical and crimson. In the anime, the Higgs energy emitted by the Guardians is blue, whereas the energy emitted by Benisuzume is red.
Hero Killer: As Benisuzume-type Gauna 490, she probably generates more human deaths than any other Gauna in the manga, wiping out a squadron and a half by itself in one sortie.
Heroic Sacrifice: Shizuka is assimilated while knocking a shell-shocked Nagate out of the way of a Gauna.
Hime Cut: Her hairstyle is a mix between this and a Scifi Bob Haircut, since it doesn't even reach her shoulders.
Humanoid Abomination: As Benisuzume, she is a trio of Gauna replicating Hoshijiro and her Guardian. Later on, the Benisuzume called Gauna 490 transforms into a more humanoid form with Hoshijiro's face.
Human Aliens: The placenta copies possess a replica human skeletal structure and organs.
Law of Chromatic Superiority: The blood-red Benisuzume-type Gauna 490 vastly outperforms every Guardian pilot except Nagate.
Lightning Bruiser: Of the three Benisuzume, Gauna 490 was even faster, stronger, and more skilled than 489 and 491, enabling it to become a reoccurring antagonist. It's even capable out out-dogfighting Nagate.
Lovecraftian Superpower: The Benisuzume were capable of projecting tentacles, firing energy beams, and shapeshifting. Their main bodies resembled a biomechanical Guardian with a skull for a cockpit, and their placenta pilots are clad in biomechanical exoskeletons resembling Guarde pilot suits.
Luminescent Blush: When she was forced to filter her urine to give a dehydrated Nagate water to drink, and following that every other romantic moment they had together leading up to her death.
Man Child: Guana 491's pilot placenta's activities - when not floating in midair and staring at the Kabi spear containment area - consisted of sounding out Nagate's name syllable by syllable, and writing it on the walls of her chamber. She even seemed dismayed when she accidentally snapped a felt pen with a tentacle while doing so and tried to fix it by putting the two halves together, like a child would. It makes what Ochiai did to her all the more disgusting.
Matryoshka Object: When not floating outside, Benisuzume's pilot placentas are seated in a cockpit-like cavity within their Guardian-shaped main bodies.
Monster Is a Mommy: The first captured placenta copy is impregnated by Ochiai and gives birth to Tsumugi and Kanata.
Now or Never Kiss: After Gauna 490 corners Nagate and is about to kill him, it sticks its naked pilot placenta into his cockpit and kisses him in order to keep him from fighting back. Nagate's fellow pilot Tsuruuchi later snarked that he was surprised Nagate didn't jump her then and there.
Not Quite Dead: Gauna 490 was seemingly killed by Nagate during the mission to stop a Mass Union Ship from smashing an asteroid into the Sidonia, but later reformed.
Official Kiss: Gauna 490 gives Nagate his first kiss while trying to kill him.
Organic Technology: Benisuzume's main body is a blood-red and white biomechanical replica of Hoshijiro's Guardian with a skull for a cockpit note , and its Pilot placenta is often dressed in a red organic version of the Guardian pilot uniforms.
Put on a Bus: The first captured replica seemed to retain some of Hoshijiro's memories of Nagate, but is seized by Ochiai before that can be explored. The second replica pilot is left in Tanikaze's cockpit when Benisuzume is destroyed, but is put in a facility well outside Ochiai's reach. It's stated that although the Benisuzume Pilot is a replicate of her, it will briefly regain her memory and identity when the Gauna core loses its control when rebuilding the placenta structure, hinting that the Gauna 490's Pilot may have fully gained Hoshijiro's memory.
Put the "Laughter" in "Slaughter": Aside from listing a kill score, Gauna 490 was laughing eerily while it utterly decimated every Guardian it went up against.
Red Baron: The Red Sphingidae/Hawkmoth, Benisuzume.
Rescue Romance: Her relationship with Nagate begins with him rescuing her after she ejects from her Guardian, and their subsequent rescue by Sidonia's defense team.
Skull for a Head: Benisuzume's cockpit resembles a skull.
Sole Survivor: Of the three Benisuzume, Gauna 490 was the only survivor of their first sortie and becomes a reoccurring threat until Nagate and Tsumugi finally defeat her.
Tragic Monster: She was Nagate's first love interest, and even after becoming a Gauna she retains traces of her human self that manifest from time to time. Chapter 21 opens with a shot of GA 490 standing in the Ocarina Mass Union Ship, with its Placenta Pilot removing her helmet to reveal a sad expression bordering on a Thousand-Yard Stare.
Twin Telepathy: 491's placenta copy had its gaze fixed on where the Kobizashi spears were stored, and the anime implies she was transmitting this intel to 490.
Woman in White: The first placenta copy morphs its half-destroyed combat exoskeleton into a white-and-red dress when Nagate visits it for the last time. Numinote  asks if he wants to enter the containment chamber.
Before what Ochiai did is revealed, that placenta is shown to have morphed a longer, more beautiful dress. Turns out that dress is just cover for the Body Horror ahead.

The highest-ranked trainee in Nagate's class and heir to Kunato Industries, the company developing the Type 18 Guardians that compose most of Sidonia's main force at the start of the series. An arrogant and vain man with little respect for his peers, Kunato develops a rivalry with Nagate due to him being assigned the Tsugumori, who he viewed as rightfully his. He sees Nagate as a thief of his glory and takes every opportunity he can to hurt or embarrass him. This culminates in him sabotaging a mission that results in Hoshijiro's death and assimilation by Gauna.
After retiring from being a pilot to focus on his father's company, Kunato undergoes emotional turmoil when he realizes that Nagate still accepts him, even if he can't forgive him for causing Hoshijiro's death. While trying to make amends and find technology that could help Sidonia, his body is secretly hijacked by the mind of Ochiai.

Ambition Is Evil: Just listen to him talking to himself about what Nagate took from him.
Artistic License - Military/Artistic License - Law: Kunato was able to pin the blame for the deaths caused by his sabotage on Nagate apparently due to no one bothering to check the flight recorders from any of the Gardes in his squad, which should have easily shown that he switched over to a private transmission to Nagate.
Catapult Nightmare: In the anime he wakes up screaming after having a dream about Benisuzume exacting revenge on him.
Engineered Heroics: Kunato sabotages a mission in a way that makes Tanikaze look at fault. As mentioned, doing so also ends up getting Hoshijiro killed.
Green-Eyed Monster: He's intensely jealous of Nagate for getting to pilot the Tsugumori and eventually becoming more famous than him. This jealous results in Hoshijiro's demise, the rise of the Crimson Hawk Moth, and eventually allowing Ochiai's mind to take his body.
Grand Theft Me: He has been completely taken over by Ochiai's original evil persona.
Heel Face Door Slam: Kunato's attempts to redeem himself backfire when he enters one of Ochiai's hidden labs and is taken over by him.
It's All About Me: Kunato was extremely arrogant and entitled, believing that only he had the right to pilot the Tsugumori.
Jerk Ass: Quite a lot, and just as he starts to undergo Character Development he's hijacked by Ochiai and becomes even worse.
Meaningful Name: Both Nori and Mozuku are types of seaweeds.
My God, What Have I Done?: Seeing Benisuzume in action sends him into a Villainous BSOD in the anime, and after Nagate tells Kunato that he still wants to fight alongside him as a pilot even though he can't forgive him for causing Hoshijiro's death, Kunato is moved to tears. The chapter this happens in is even named "Kunato Norio's Emotional Turmoil".
Netorare: Kunato's relationship to Hoshijiro and Nagate has shades of this, particularly after Ochiai takes over and creates Tsumugi out of the Hoshijiro placenta.
Nice Job Breaking It, Hero: His sabotage of a mission to discredit Nagate was not only petty, but put En in a coma and - far worse - resulted in Hoshijiro being assimilated into the Gauna and becoming Benisuzume. It also lead to the deaths of multiple other pilots due to the Gauna's tail they were suppose to sever still being attached and able to attack.
Screw the Rules, I Have Connections!: Gets away with neglecting his duties as trainee representative and injuring fellow trainees thanks to the influence of his family.

Norio's relative and voice of conscience. She is murdered by Ochiai's doll and resurrected as his puppet.
Killed Off for Real: She hijacks a Guardian in order to assist Kanata's breakout and is shot down by Samari.
Only Mostly Dead: Her body survives thanks to the reinforced cockpit of the Guardian.
Meaningful Name: Both Nori and Mozuku are types of seaweeds.
Morality Pet: She functioned as Norio's voice of conscience.
Number Two: She was this to Norio, and later The Dragon for Ochiai.
Off with His Head!: She's decapitated and dismembered by Ochiai's doll while examining some cacti.
Restraining Bolt: As Tsumugi's "pilot", her main purpose was to stop Tsumugi from turning on Sidonia.
The Stoic: After being resurrected she has a perpetually emotionless expression.
Traumatic Haircut: Cut her long hair after she was resurrected.
The Undead: She was decapitated and dismembered, through Ochiai stitched her back up and resurrected her.

A bright and calculating girl, Yuhata becomes a friend of Izana and Nagate after the latter terminates the Gauna that killed her brother, a member of Akai's squad. Quickly developing feelings for Nagate, she constantly competes with Izana for his attention.
Yuhata later becomes the assistant commander for Guardian operations due to her talent for battle tactics.
Clingy Jealous Girl: She is quite possessive of Nagate, sneering behind his back when he invites Shizuka and Izana on a trip to Sidonia's ocean and trying to rig the underwater pods so that they would be left out. It backfires, and she's left stuck with Izana.
Colourful Theme Naming: Midori is the Japanese term for green.
The Captain: Of the warship Mizuki.
Innocent Cohabitation: She joins Izana and Tsumugi as one of Nagate's housemates.
Number Two: She becomes this to Kobayashi after Ichirou Seii returns to the field. She's later promoted to Vice-Commander.
The Strategist: Ichirou Seii, the prior Commander's Aide, takes note of her strategic brilliance and handpicks her as his successor.
You Gotta Have Blue Hair: Yuhata has green hair.
Young and in Charge: One of the youngest human characters and already assistant commander and later captain of the Mizuki.