The euphoric homeostasis our protagonist Akiha enjoys while eating her breakfast is shattered when she has explained to her Kazane's marriage volition. Nami's derisive remark and Kazane having created several designs for the wedding gown prompts Akiha to recruit Imoko into her plans to vote with her feet. Galvanized by the prospect of an amplified allowance, Nami gives chase and tries to scare capitulation into Akiha only to find that Imoko has already steered for the space port where Akiha finds that she cannot board the transport due to not having her student card, a minor but unexpected setback that stops the agoraphobic Nami in her tracks. Imoko and Akiha drive to the school with two of Akiha's classmates, one of which secures an escape pod for Akiha which she and Imoko avail after school only to be caught in the midst of a gravity quake, a gravity quake caused by the brain colony Leopard phasing in from hyperspace. Ahika exploring around on Leopard before meeting the AI entity face-to-face sets the stage for a frenzied Othello sequence that introduces Itsuki Kannagi (who tries to arrest both Akiha and Leopard), the QT-Arms Starsylph (which Akiha uses to arrest Leopard's ballistic plummet with Itsuki's guidance), and Honoka Kawai (who seems to have been awaiting Akiha's arrival along with Akiha's other siblings Takane and Sakura.

The hullabaloo from Leopard's antics from the previous episode obfuscates Itsuki's computations of her prologue prior to being recalled by her supervisor along with Akiha having a dream after her classmate Julio rescues her from floating in space. Nami teases Akiha before running into Kazane who (after ordering Nami to her room) offers her apologies for the adverse side effects of her actions. It seems that the Student Council president wants to confront Akiha for her earlier adventure in the escape pod, a volition with which Honoka violently disagrees as she introduces herself in earnest. While Itsuki and Nina compute their next move regarding Leopard with UL, Honoka abducts Akiha and explains that she has an important role to fulfill for Leopard before leading her through equipping and defining the Q-TECTOR as the two set off on their first mission, replacing the magnetic chamber to Leopard's antimatter cannon. While Akiha grapples with the ethics, Honoka simply orders Wygar to destroy whatever precludes their travel path not caring that she brings the ICP into the mix by doing so. Directing that Akiha proceed on ahead, Honoka challenges Itsuki who soundly defeats her before confronting Akiha who is just about to emancipate the Golden Orb for transport, that is, if a clear trajectory can first be entreated of the newly-arrived Nervalist annelid.

Wrapping itself around the Golden Orb, the Nervalist annelid wastes no time initiating its "This stays right here, interlopers!" attack. Honoka capitalizes upon Itsuki's decoy act and successfully wounds the annelid before helping Akiha transport the Golden Orb to Leopard in spite of Itsuki's injunction. Seeing the Nervalist annelid refuse to accept defeat as it orders the whole facility to give chase, Honoka stays behind and directs Akiha on ahead whose computations on interpreting the circumstances quickly takes a back seat to the converging ICP. The Golden Orb now in place, Leopard prepares to discharge his Golden Soul Shout; an effulgent explosion later, Leopard celebrating his victory with a haiku prompts Imoko to savagely remonstrate the AI entity and Akiha to repudiate Leopard much to Honoka's anguish. Meanwhile, Itsuki's decision to take matters into her own hands in spite of being read the riot act inspires the ICP powers-that-be to charge Bougainvillea and Mintao Itsuki's capture, the first attempt thereof blowing up in their face thanks to Itsuki's supervisor Nina. Even with her undercover alias Mutsumi Shimoyama, Itsuki demonstrates several times that she needs to be polished in several areas. Unfortunately, Honoka still sees the entire ICP as her enemy and decides to confront Itsuki by first luring her to the roof for a one-on-one duel. Shocked at the temerity behind Honoka's absolute neutrality injunction considering the damage caused thus far, Akiha intercedes with a "Stop this at once!" smack to both Honoka and Itsuki.

Amid the effulgent camera flashbulbs galvanized by the fanatical and frenzied volition for the ideal photograph, Akiha has her reservations about the mission objective which Honoka promptly replies with a "Not another word about the ICP!" telekinetic sweep that knocks Akiha on her bottom unaware that she is what Bougainvillea and Mintao are having a briefing complete with an injunction about the Shishido family. While Itsuki is cautioned about Bougainvillea and Mintao, Leopard's web-surfing on her computer incenses Akiha enough to confront the AI and declare her autonomy only to have the mission objective reaffirmed, acquiring the Positron Matrix, before being sent on her way with Imoko. Meanwhile, Itsuki is summoned when a psychotic Nervalist iconoclast decides to wreak havoc only to find that she cannot even defend herself, never mind attacking him. Several members of the Student Council combining efforts with Honoka to stalemate and eventually neutralize the assailant sets the stage for a sequence that explains the common prologue both Honoka and Itsuki share with the Nervalists and the X-QT race, the latter having a near-complete computation crash as she tries to interpret all she has experienced while the ICP deals with the aftermath. Leopard reads Akiha finding the Positron Matrix right when Itsuki arrests her as the perfect opportunity to humble Akiha's recalcitrance by phasing away parts of her Q-TECTOR. Unfortunately, since Itsuki is in the same boat, that forces an armistice as Akiha and Itsuki collaborate to evacuate with some of their dignity and modesty unaware that Honoka has already successfully acquired the mission objective.

While Honoka goes over the specification registry and finds that there are a lot of absent but necessary components, Akiha barging in with a "How dare you debase and subjugate me!" kick to the casing before storming away after reading the aristocratic AI the riot act gives way to Kazane hosting an emergency meeting with the Shishido Trustees regarding the X-QT bounty hunter Aleida wiping out Takane's team and the Nervalists capturing Sakura with the volition of wielding the child genius for their own ends. Her anger at Leopard gone, Akiha sets to her daily school life and appears to be much happier. Honoka approaches Akiha with an entreaty to reconsider her repudiation that suggests that she has no independent human volition as she relays Akiha's inquiry of why Leopard chose her. Sakura introducing herself in earnest through a payload she sent to the Shishido family gives way to Itsuki delivering a "To the colony, or else!" gunpoint nudge that places them before Bougainvillea and Mintao who are charged Itsuki's apprehension. The deus ex machina comes when Leopard manifests himself and Honoka enters the fight to assist Itsuki. After Akiha has Starsylph embarrass Bougainvillea and Mintao before sending the two ninja flying, Leopard and Akiha's mutual interdependence on each other and Itsuki being a trustworthy ally are both confirmed quod erat demonstrandum.

While Leopard amuses himself by conducting a radio show, Kazane is concerned that Takane's reports have stopped flowing and orders that things be played by ear while Honoka shows Akiha and Itsuki the St. Artemis criminal corrections facility on the Moon where a part for Leopard is kept inside a perimeter of alarms before leading the way into the facility where she promptly loses her way. UL quickly locates the group's destination but accidentally instigates a prison riot that brings Bougainvillea and Mintao into the mix. While Akiha tries to swim out of the stampeding prisoners, Itsuki and Honoka encounter Sakura's personal bodyguard that wishes to befriend the pair; a brief but fierce battle gives way to an encounter with the charming and affectionate Sakura. Akiha rejoins the group in time for a video feed depicting Takane as Aleida's prisoner and rushes off to the rescue with Honoka and Itsuki right on her heels. Aleida stalemating Honoka gives way to Leopard's sudden arrival -- and Nerval's awakening from a protracted estivation that has amplified a fierce long-standing vendetta.

As Nerval advances toward Leopard in preparation to do battle, Aleida takes off with Takane. Frightened for Takane's safety, Akiha leads the way to the QT-Arms with Honoka and Itsuki right on her heels. Bougainvillea and Mintao intercept Itsuki only to get caught up in Nerval deep-freezing Leopard. While Kazane is appointed alpha administrator and given Morihime, Akiha and Honoka fare no better as they rush to the rescue. Nerval and Aleida accosting the group drives Honoka into a frenzy that inspires Takane to intercede. A big hullabaloo breaks out whose deus ex machina comes when Sakura reasons that sunlight can emancipate Leopard from his icy prison. Kazane and Takane's combined intercession paves the way for Akiha to finish off Nerval. Unfortunately, Xanthippe phases in to carry off Nerval who vows vengeance at next engagement. Akiha's bewilderment at the recent events nearly becomes a comprehensive cerebral computation crash when Kazane and Elle explain that she was born into a family whose role in constructing Nerval and all the brain colonies that came thereafter includes being charged military vigilance thereof -- in this case, against Nerval.

As Akiha scrambles to interpret the colossal and momentous stewardship she has been charged, Honoka declares her visceral objection but relents after she realizes that the Shishido family is not the adversary Nerval is before leading everybody to Leopard. As Sakura has demonstrated for her, Leopard is not thrilled with having company disrupt his computation of Nerval and Xanthippe's next move and the necessary countermeasures thereof -- especially if that company wishes to add a woman's touch like Kazane and Takane. While bathing in the hot spring, Kazane explaining the prologue of the Shishido family and the brain colonies like Leopard gives way to a Crocodilas leaping onto the scene to steal the Golden Orb's cooling system and the research adventure in the library defined by a knight that is none too thrilled to have visitors. Itsuki inhibits the knight long enough to discern its volition and define the group as its allies; after a protracted messy search, the requisite map is in hand and the chase continues. It seems that the Crocodilas took the cooling system to avail as a plaything for its child relatives; while a gentle explanation is enough to retrieve the stolen cooling system, it does not keep Bougainvillea and Mintao from getting read the riot act for their damaged QT-Arms and their unsuccessful capture of Itsuki.

This episode is a parallel alternate reality that expounds more upon the QT force using baseball as the demonstration forum. Consequently, Honoka plays the role of catcher/contract administrator while Akiha conducts herself as a mysterious pitcher that has been endowed with QT powers. The plot wields Itsuki as an orphan with dormant QT powers that has traded baseball for a career as an office lady and charges her an important stewardship: extinguishing Akiha's rampage of revenge. Itsuki is able to stalemate Akiha at her first confrontation due to the structural damage accumulated by the latter reaching critical mass. While Akiha's prologue is explained prior to the doctor's arrival, Itsuki approaches the baseball demon Leopard for his instruction which comes at a high price. Ultimately, Itsuki and Akiha learn that they have both been wielded as tools that have outlived their usefulness.

The revelation that Nina is reinstating Itsuki back to active ICP duty gives way to the discovery of a box with a girl inside that later shows up at Akiha's school that offers data about Enigma for asylum. Akiha computing her next move obfuscates Leopard's bewildered disdain at an upgrade Sakura built that earns him a stern reprimand from Kazane who adds her displeasure at Akiha being wielded as his servant along with Honoka who apparently has a profound prologue with the Shishido family Senate. Akiha is conscripted into an exciting adventure at school when the box is mistaken for trash that ends with a timely gunshot from Itsuki and Emilio's intercession. Honoka explains that the box houses a renegade Nervalist that has had her human individuality sealed away as the group returns to Akiha's house for a sleepover as they await Kazane's return. Unfortunately, Aleida attacks the Shishido family in a bid to retrieve the box and succeeds with her retrieval mission in spite of Kazane and Takane's combined intercession.

After recovering herself and dusting herself off, Akiha has it explained to her that there is a thief stealing Energizer Mirrors that Kazane and Takane suspect is an ally of Nerval. Because of the limited data and unknown resource requirements, Kazane directs Akiha and Imoko to school along with a promise from Takane to apprise of any new discoveries. While Honoka and Akiha change course to Leopard who is not thrilled with Sakura's attempts to entertain herself at his expense, it seems that there is something rotten in the Surre Academy Student Council as Aleida introduces Tsutsuji Baba to the AI entity Benkei along with there being quite a prologue between Aleida and Tsutsuji. As Benkei explains the Bisner Plan to Tsutsuji, Kazane manifests her displeasure at Akiha skipping school by lashing out at Nami who is incensed at being kept out of the loop with a stern "Stop whining and grow up already!" tirade before she and Takane make their exit. While out and about, Nami has a psychotic nervous breakdown related to her prologue as a model along with the anguish of being estranged from her family that sets the stage for her defection to Nerval whose volition for her is similar to that of Leopard for Akiha. The ICP powers-that-be wield Itsuki in a grudge match against Bougainvillea and Mintao who are following orders from the Shishido family to avail mirrors as bait to lure out Benkei who promptly phases into normal space.

Everybody watches spellbound with her own perspective as Benkei brags about his current corporeal form and greets Leopard whose inability to recall their collaborative history prompts Benkei to ram Leopard. While Akiha and Imoko recover themselves, Takane and Honoka rush out to infiltrate Benkei whose argument with Leopard is an equal mix of Benkei's mirror theft attempts being repelled and rapier ripostes between both brain colonies. Tsutsuji's declaration of war against fate (aka Akiha herself) gives way to Itsuki joining the battle with Kazane's approval. Benkei encasing Leopard in an airtight matrix escalates matters to require the Leopard Cannon as well as the Absolute Break Through Control, both of which Benkei perverts to his advantage and Kirkwood's detriment. It seems that Tsutsuji initiating an energy signal that overrides autonomous human volition is part of Nerval's revenge from the St. Artemis battle, stalemating/subjugating Leopard, conquering the Shishido family, and arrogating Kirkwood. Furious at being wielded in Nerval's plans, Leopard recovers himself to push Benkei into a decaying orbit above Earth before ejecting himself. Takane, now a Nervalist vassal, wields her QT-ARMS to inhibit Akiha's collaborative efforts with Honoka and Itsuki to arrest Leopard's kamikaze plummet with Benkei.

While waiting for Imoko to get Starsylph back in the air, Akiha revels in the contrast between Earth and Kirkwood while computing her next move to locate everybody. Leopard having safely touched down gives way to a high downhill/white-water adventure in which Akiha soundly and thoroughly remonstrates Leopard's selfishness. Itsuki advising Honoka against treating her QT powers like a universal skeleton key takes a back seat to Akiha and Imoko arriving in Starsylph with Leopard. As Leopard floats down the river with the three girls, they find their route lined with observers. Itsuki shares a bit of her prologue as she leads Akiha and Honoka through a destroyed botanical garden only to find themselves surrounded by a hostile indigenous tribe that wishes vengeance on an entity that effected the Terra Abduction. Unfortunately for Honoka, the tribe gladly settles for her as a consolation prize, the rationale thereof come forthwith. Honoka's dysphoric prologue is exhibited while Honoka easily dispenses with the situation and scolds Akiha for her weak heart before Sakura shows up to transport the trio along with Leopard to safety. Upon encountering an old man named Friedrich Otto Noblemain that uses a QT rose to entrap their craft for his own use, Honoka leaps into action to extinguish her dysphoric prologue.

After Akiha and Itsuki pull her away from him, Friedrich refutes Honoka's imputes of cowardice before offering his hospitality but not the sought-after technique for returning to space Leopard and the girls are searching for. Tsutsuji's conclusion that Nerval is not coming to the rescue along with her subsequent decision to wield the indigenous tribe in a raid to capture Sakura's ship obfuscates the difficult time Kirkwood is having while Aleida continues her efforts to pollute Nami's computations so that she becomes the Nervalist "girl who leaps through space" of her own volition. Nina approaching Bougainvillea and Mintao who are moved to tears that she actually treats them like human beings while inviting them to join the Mysteries Division obfuscates Itsuki (who suspects that Friedrich knows more than he says) having it explained that the Pied Piper (the mysterious structure that appears to hypnotize people) is actually an orbital elevator for gathering people to become Nerval's colonists and have it demonstrated that the QT rose's primary purpose is as a defensive counter-measure. The Pied Piper successfully repulsed, Friedrich explains that he unplugged several components from Leopard for fear that he would betray humanity, the same components that Akiha and Honoka have been out and about retrieving. Akiha barely has a chance to ask the significance of the "girl who leaps through spacee" before Tsutsuji and Benkei make their move to hijack Sakura's ship only to learn that the Pied Piper orbital elevator more than meets their needs in this regard right as Nami is flown off to be empowered as a "girl who leaps through space".

The ship now repaired along with Friedrich's counsel of when and where the Pied Piper will again appear, Sakura and Honoka having satisfactorily manifested their divergent perspectives regarding Tsutsuji and Benkei's propitiation before Akiha gives way to Friedrich giving everybody some seedlings of the QT-rose to guard against the Existences' psycho wave as a bon voyage gift prior to the hectic adventure of entering the Pied Piper. Bougainvillea and Mintao discovering the seriously-injured Elle while on patrol and Nina congratulating them obfuscates Akiha and the gang having the Terra Abduction demonstrated for them along with Xanthippe phasing in from hyperspace to greet Aleida prior to collecting the newly-captured prisoners from Pied Piper. Sakura spotting Nami sends Akiha into a mad dash to her QT-Arms for some answers with Itsuki and Honoka right on her heels . . . just in time to see Nami reaching for the mystical staff Aleida is offering. Akiha exhorts Nami's company only to find that Nami's computations are thoroughly polluted and that she is Nami's alpha vendetta. While the Existence octet bootstrap themselves for battle, Itsuki and Honoka arrive to learn Aleida's real identity and that Nami has repudiated the entire Shishido family. Sakura slicing at Xanthippe's hull disrupts Nami's preparation to finish off Akiha who makes a hasty retreat. After ordering the Existence octet to effect a cerebral crash on Leopard, Nami and Aleida board Xanthippe as she phases into hyperspace to Akiha's anguish .

As the Nervalist siege on Kirkwood continues, the Surre Academy students do what they can to cope. Emilio leads the Student Council through smuggling themselves out of the school -- and right into a confrontation with a Nervalist automaton that promptly gives chase with several of its brethern. The ICP facilitating the evacuation only to find themselves the vendetta of the Remote Attackers obfuscates Nerval having a housekeeping conference with his subordinates while in an anthropoid form prior to Xanthippe's arrival with Nami and Aleida. While the missing-in-action Kazane is shown safe and sound on the Moon with Morihime listening in on the aftermath of Nerval's political maneuvering, Nami meeting Nerval for the first time turns out to be quite an adventure. While Nami and Nerval reconcile their expectations of each other to reality, Akiha recovers herself and is shocked to find that her reckless attempt to chase Nami has gotten her thrown into orbit around Jupiter much to her shock. UL's tabulation of an estimated travel time back to Kirkwood of five years and the oxygen supply lasting ten years gives way to a triangular argument that is only disrupted by Tsutsuji and Benkei's hijacking attempt along with Sakura discovering both the Leopard and Benkei Colonies intact. After Leopard is installed back in his colony body, Honoka and Itsuki seclude themselves to sort out their feelings while Leopard angers Akiha with the misogynist accusation of inevitable treachery »inherent« to the Shishido family -- right until the advent of a mysterious electrical storm within the colony . . .

Engulfed by the electrical storm, Leopard's colony begins falling towards Jupiter. Sakura's scarf and hat reveals itself as an alien named Yupitan, and suggests using the Benkei colony (which is still attacked to Leopard's colony as a result of their fight) to provide the additional acceleration needed to escape from Jupiter's gravity well. With help from Tsutsuji and the QT-Arms, the plan is successful, and they come across an abandoned space station. Yupitan tells them it was the old base of the Shishido family when they were fighting Nerval, and they discover that the energy stored there will allow them to hyperjump back to Kirkwood. However, Loepard refuses to hyperjump, so they get Benkei to do it instead. At the refugees, Bou and Min are assigned to help infiltrate Surre Academy, but they see Nami brutally force one of the students into a box and run away, leading the Nervalist forces to the refugees. As Nami leads an assault on them, Leopard and Benkei suddenly appear.

Seeing Leopard, Nami is stunned, and when Akiha races towards her, Nami commands the Nervalist forces to retreat. Seeing his chance, Benkei separates from Leopard, and steals two of Leopard's mirrors before escaping. Akiha, Honoka, and Itsuki meet with Elle and Emilio, who decide to transfer as many people as possible to Leopard's colony. Due to the Existence attack, Leopard is still unable to connect to his colony, so Akiha tries to cheer him up, but fails. With pressure from Elle and advice from Itsuki, they hold a party to cheer Leopard up. After the party, Leopard and Akiha share a private moment looking up at the Earth and the Moon, and have a heart-to-heart talk. Akiha shows Leopard that everyone is encouraging him, and Leopard is able to connect to his colony again just as Xanthippe attacks. He successfully fights her off with the Leopard cannon, but in the aftermath, Akiha is kidnapped by Aleida.

Hiding out inside a volcanic asteroid, Tsutsuji and Benkei are ambushed by Leopard, who takes back his mirrors. As everyone investigates Akiha's kidnapping, Leopard wants to chase after Nerval immediately, but the citizens are anxious about power failures. Nina orders Bou and Min to investigate the colony underground with Itsuki's guidance, and they soon find a hot spring. While relaxing in the hot spring, they are attacked by an octopus-like creature, which captures Bou and Min. Itsuki escapes and warns everyone to evacuate, but is captured herself until Kazane, newly arrived, rescues everyone. Akiha and Imoko find themselves inside Xanthippe, and attempt to escape, only to find that the colony contains row upon row of boxes, as elsewhere Nerval shows a factory responsible for creating the boxes to Nami. Xanthippe declares that humans are merely the component parts of brain colonies. Akiha tries to run, but the box humans report her, and she is captured and forced into a box.

Aboard Xanthippe, Akiha wakes up inside her box, with Imo-chan still trying to get her out and Leopard still searching for her. After Akiha's friends return from an unsuccessful search, they decide that Akiha must be in Kirkwood. However, Honoka collapses soon after, and reveals that her lifespan is nearly over. In the meantime, Kazane talks with Leopard, discussing how they can find Leopard's last three parts. When Benkei shows up to challenge Leopard again, Kazane successfully negotiates with Tsutsuji for the pair to retrieve the Proxima Crown for Leopard.

Leopard arrives at the Innsmouth Reef. Though he still wants to retrieve Akiha before anything else, Kazane keeps him searching for the Sword, one of the last three parts he needs. Akiha, meanwhile, is still trapped in the box, but has figured out how to get food and drink and starts to grow accustomed to the box, causing Imo-chan to worry. Elsewhere, Nami wakes up in the Cafe Enigma and finds Nerval making food on an old-fashioned stove, and Aleida soon shows up to help. However, he angers Nami when he tells her that Akiha will soon come to the Cafe, and she storms out.

Akiha is rescued by Itsuki, but the student council ship is pursued by Nervalists and forced to take shelter in Kirkwood. The UURE, which has taken over the moon, is planning another attack. However, their plan is interrupted by Nerval, who appears and freezes the whole moon. On Earth, Honoka gets Fon to come with her by hitting him with a bowling pin and kidnapping him. Akiha can't come to grips with Imo-chan being gone, but she, Itsuki and the student council find a box human factory and meet up with one of the Shishido elders.

With Leopard connected to the Proxima Crown that Benkei found, the Shishido elders volunteer to search for the sword. Nerval instructs Xanthippe to destroy Leopard and Aleida to kidnap Akiha, while Takane is told to protect Akiha. Akiha is still in mourning for Imo-chan, and runs away when Itsuki tries to comfort her. She goes to Leopard's core to talk to him, but Leopard's inconsiderate words only make Akiha mad, just as Xanthippe appears. Aleida successfully breaks into Leopard, but Takane prevents her from kidnapping Akiha. Itsuki then rescues Akiha from box people, but they are attacked by the Existence.

Xanthippe reveals that Nerval was the one who actually destroyed the missile that everyone thought Imo-chan had rammed, and that he transported Imo-chan to him. Akiha is determined to rescue Imo-chan, but Kazane stops her. Leopard exults over his competition, and begins a conversion with Dark Leopard, his alter ego.

Nerval explains to Imo-chan that this is Leopard's true appearance, as Imo-chan wonders which side she should be on. The refugees begin evacuating Leopard, as Leopard and Nerval fight. After an exchange of fire, Nerval is heavily damage. Akiha leaves to try to rescue Imo-chan, but Nerval flees, and Akiha and Nami meet near Cafe Enigma.

Kazane goes over the plan to stop Leopard, assigning Akiha and Honoka to the job of attacking the brain, with the help of the Existence. Kagura asks to be allowed to deal with Nami, because she sees much of herself in Nami. Kagura confronts Nami, and tries to talk Nami out of fighting, but fails and is forced to defeat Nami. As everyone helps with the attack on Leopard, Akiha, Honoka, and the Existence break into Leopard itself as Sakura and the Shishido elders prepare to disable Leopard's power supply and QT-Roses, but Leopard moves and prepares to fire the cannon. He also creates a hyperspace rupture that prevents Akiha from reaching his core.