Setting The game's story primarily focuses on the exploits of the space-faring organization known as Oracle, who uses Photons to traverse the universe and seek new planets for potential colonization while simultaneously suppressing the threat of the Falspawn, alien beings created by evil entities known as Dark Falz that only exist to destroy the universe. Oracle is split between a Mothership, housing the fleet's central core, and a massive fleet of spaceships that contains all civilian entities and the fleet's prime military and exploration department known as ARKS (Artificial Relicit to Keep Species). Initially, ARKS is sent to investigate activity on three planets: Naverius, a planet whose ecosystem was primarily forest before much of the planet became locked in eternal winter, Lillipa, a desert planet inhabited by rabbit-like natives known as "Lillipans", and Amduskia, a bifurcated planet with a volcanic core surrounded by a mass of floating islands inhabited by humanoid dragonfolk. Later story arcs feature the planet Wopal, an ocean planet, and Harukotan, a planet in the shape of a
taijitu inhabited by two opposing races. In
EPISODE 4, exploration expands to encompass a fictional counterpart of Earth located in an alternate dimension, and in
EPISODE 5, an alternate dimension known as "Omega" located within a black hole becomes the focal point of the story.
Phantasy Star Online 2: New Genesis takes place 1,000 years after the events of
Phantasy Star Online 2. The game's story takes place in the planet, Halpha. A new generation of ARKS are Meteorns, people who have landed to a planet via a drop pod, who had advanced techniques, using Photons, to run faster, jump higher and glide between distances. They are also sworn to fight a new enemy, the DOLLS. In Episode 2 Chapter 1 (Chapter 6), they fight against a new enemy, the Starless.
Story Phantasy Star Online 2 Oracle Arc Episode 1 The story follows the player character, a graduating member of the ARKS Cadet program, and their partner Afin. During their graduation exercise on Naverius, the Cadets are attacked by the Falspawn, forcing ARKS veterans Zeno and Echo to arrive and rescue the player and Afin. Upon arriving on the ARKS Ship, the player encounters a woman named Xion, who grants the player a Divergence Matrix, an artifact with the ability to alter fate. Returning to Naverius to investigate the Falspawn, the player rescues a girl named Matoi, who has apparent amnesia, and sends her to the ARKS Ship to recover. The player is sent out to various planets to investigate Falspawn activity. During their travels, they discover the fragments weapon called the Clarissa, one of a series of weapons known as a Cosmogenic Arm, and collect its pieces while being pursued by a mysterious foe called "Persona". The player successfully gathers the Clarissa fragments and entrusts the weapon to weaponsmith Zig for repairs, but the weapon is stolen by ARKS operatives Gettemhult and Melphonsena. The player, Zeno, and Echo pursue them to Naverius, where Gettemhult revives Dark Falz [Elder] and is subsequently possessed. Zeno stays behind to allow the player, Echo, and Melphonsena to escape and is presumed dead.
Episode 2 Returning to the ARKS Ship, the player and Xion meet Luther, the leader of ARKS and last member of an ancient race known as the "Photoners". During a visit to Wopal, the player witnesses Luther manipulating and recruiting Theodore, an ARKS member who was driven insane by the death of his girlfriend Ulku. The player travels to Amduskia to meet Xiao, an imperfect clone of Xion, and is granted the ability to time travel to disrupt Luther's plans by rescuing Zeno and Ulku in the past. Xion urges the player and Matoi to head to the Mothership to rescue her, but the duo are branded traitors of ARKS by Regius, a member of an elite ARKS unit called the Six Pillars, and are hunted down by fellow ARKS. The player and Matoi discover that Luther plans to assimilate Xion and gain omniscience. The duo, aided by other members of the Six Pillars and Ulku, rescues Theodore and presses on to the Mothership's core, where Xion convinces the party to kill her. Luther, enraged by his loss, transforms into Dark Falz [Luther] and possesses the Mothership. Xiao rescues the Oracle fleet by manifesting another Mothership and the party escapes. ARKS confronts and defeats Dark Falz [Luther], and his body is consumed by another Dark Falz, Dark Falz [Gemini].
Episode 3 Xiao soon sends the player and Matoi to the planet Harukotan to investigate [Gemini]'s suspicious activity. While there, the duo befriend Sukuna-hime, a local deity, and together they fend off [Gemini]'s attacks. Due to civil war brewing on the planet, Sukuna-hime decides to confront the Nightfaller King, but she is ambushed by [Gemini] and the player and Matoi and are consumed while trying to save her. While in [Gemini], they discover that Luther has survived by being consumed by [Gemini], and he reveals that [Gemini] wants to revive the [Profound Darkness], an ancient enemy of the Photoners and the progenitor of the Dark Falz. The player and Matoi escape and confront [Gemini], but as they are dying [Gemini] infects Matoi with a large quantity of F-Factor, causing her to become a new [Profound Darkness]. The player is confronted by [Persona], revealed to be an alternate timeline counterpart of the player, and is coerced into killing Matoi to stop the [Profound Darkness]. However, it is revealed that by doing so, the player becomes the next [Persona]. With the aid of the Divergence Matrix, the player gathers their allies and tries to stop Matoi without killing her; [Persona], moved by the player's willingness to change fate, intervenes and absorbs Matoi's F-Factor, becoming the [Profound Darkness] in her stead. ARKS subsequently confronts and temporarily kills the [Profound Darkness]. However, since it cannot truly be killed the last part of [Persona] forcefully binds himself and the [Profound Darkness] to a time loop using their copy of the Divergence Matrix. Afterwards the player and Matoi have a bittersweet reunion where they both swear to find a way to both save [Persona] and permanently kill the [Profound Darkness].
Earth Arc Episode 4 Three years after the events of
EPISODE 3 and one year after the events of
Phantasy Star Online 2 The Animation, the player is revived from stasis by the operator Xiera to accompany a new recruit named Hitsugi, a young boy, who is suspected to have ties to an internal invasion of fake ARKS members. During the mission, Hitsugi is attacked by a mysterious black mass; the player attempts to purify Hitsugi, but Hitsugi disappears prematurely. "Hitsugi" is revealed to be a high school girl from Earth playing the video game
Phantasy Star Online 2, who finds a strange boy with her avatar's appearance in her room after the fiasco. Hitsugi names the boy "Al". The player is sent to investigate Earth, where they discover that Earth uses a parallel mutation of Photons known as "Aether" that has the ability to resonate with the emotions of humans, and "Phantasy Star Online 2" is an espionage tool disguised as a video game to allow members of a mysterious group known as Mother Corps to interface with and infiltrate ARKS. Discovering that Mother Corps is secretly plotting against ARKS, the player allies themselves with Hitsugi and her brother Enga, a member of a secret organization opposing Mother Corps called "Earth Guide", and fights off various members of Mother Corps wreaking havoc across the globe. Hitsugi manifests a weapon constructed of Aether, the
Ame-no-Habakiri, but during a confrontation against her best friend Kohri Wagashimiya, who was brainwashed by Mother Corps, it is destroyed. Kohri seemingly kills Hitsugi, but Al, revealed to be a Dark Falz, revives her, and Hitsugi is kidnapped and taken to the Moon. The player and Enga rescue Hitsugi, but discover that the player's ARKS Ship had been attacked by Mother Corps. The player and Hitsugi return to the ship, where Hitsugi witnesses Mother, the leader of Mother Corps, assimilating Al, causing Hitsugi to awaken to her true Aether weapon, the
Ame-no-Murakumo. The party returns to Earth, where Hitsugi uses her new weapon to save Kohri, and together the party confronts Mother on the Moon. Mother is revealed to be an imperfect copy of Xion discarded into space and seeks vengeance against the Photoners and ARKS. Mother is overwhelmed by the Dark Falz power she stole and transforms into a Dark Falz, but the party defeats her and returns her and Al to normal. However, the party is betrayed by Adam Sacrid, the leader of Earth Guide, who kills Mother and steals her powers. The party, aided by the remaining Mother Corps members, confront Adam in the Earth Guide sanctuary, and witness him creating
Yggdrasil in the Pacific Ocean. Adam takes the guise of a massive Phantasm monster called Deus Esca and seals the party's Aether powers while banishing the player back to the ARKS Ship. Al discovers that Mother's consciousness is still in his body, and Mother possesses him to return the player to Earth and restore the party's Aether powers. The party defeats Deus Esca and Adam, realizing the error of his ways, returns to normal before dying.
Photoner Arc Episode 5 During an attempt to destroy the [Profound Darkness] permanently by purifying [Persona], the player is sucked into an alternate dimension known as "Omega", where they rescue a young girl before escaping. Returning to the ARKS Ship, they are greeted by Alma, the deceased spirit of the first Klarisklays, who informs them that Omega is form of the fragmented Akashic Records, the source of all knowledge where Xion formerly resided, and has now manifested itself into a black hole threatening to consume the universe. In an attempt to stop the black hole, Alma grants the player the power to return to Omega at will by using her ability to stop time. Upon their return, the player reunites with the girl, named Hariette, and discovers that the continent is plagued by a strange flower called Ephemera, a manifestation of the [Profound Darkness]'s corruption. The player unites with Hariette to put an end to various schemes across Omega instigated by a mysterious foe known as Elmir. They learn that the countries of Omega are associated strongly with the Dark Falz that they had encountered previously, and during their quest the player re-encounters and defeats each of the Falzes revived in some fashion by Elmir, in the process absorbing their consciousnesses. Upon defeating the final Falz, Elmir is revealed to be an incarnation of Dark Falz [Persona], who manipulated the player into killing the Falz and returning their essences to Omega itself, revealed to be an incarnation of the [Profound Darkness]. Elmir kidnaps Hariette and seals her in a giant flower, attempting to use her and the combined Falz essences to destroy the outside world. With the help of Alma and allies from Omega, the player intervenes and defeats Elmir, killing him for good. Hariette is saved and pronounced the new goddess of Omega, and the player successfully seals the black hole.
Episode 6 After returning to the ARKS Ship, the player and their allies are attacked by the Goddess of Annihilation, Shiva, a woman with an identical appearance to Hariette, and are unable to surmount her Photon-absorbing powers. Risa, a Class Trainer on the ARKS Ship, is revealed to be in possession of Hariette, who has reincarnated in the form of a Cosmogenic Arm in the real world, and they fend off Shiva. The player learns that Shiva is an artificial Photoner and Hariette's original body who was used to seal the original form of the [Profound Darkness], but was revived by the sealing of Omega and now desires revenge by destroying the universe. Shiva mounts an attack against Mothership Xiao in a bid to steal it for herself; although ARKS is dispatched to defend against her, they are overwhelmed by her Luminmech forces and Xiao is seemingly killed, forcing ARKS to flee. The heroes return to Amduskia to revive Xiao by uniting a fragment of his power with Kasheena, a failed Xion clone whose body lies at the heart of the planet, warding off further direct attacks to Oracle. The player and Matoi return to Harukotan to help Sukuna-hime fend off Shiva's attacks and eventually attempt to fight Shiva herself by using Sukuna-hime's power to seal Shiva's abilities. Although the attempt fails, Hariette learns from Sukuna-hime how to weaken Shiva by using a similar seal within Omega to affect her on a universal scale. Hariette remains in Omega to maintain the seal while the player and Risa return to the real world. With Shiva weakened, ARKS mounts a last stand against Shiva's forces, with the player and Matoi leading the charge. Although the duo successfully reach Shiva, they are still greatly overwhelmed by her strength until Sukuna-hime intervenes at the last minute and gives them the power to deal the finishing blow. With her dying breath, Shiva transfers the essence of the [Profound Darkness] to the player, causing them to become the original form of the [Profound Darkness], the Primordial Darkness. Xion reaches out to the player and asks them to avert tragedy by traveling back to the beginning of time and becoming the Akashic Record, but the player, choosing to fight the Primordial Darkness, inspires Xion to reach out to Matoi, Hitsugi, and Hariette to unite their powers. The three heroines arrive and use the Ame-no-Murakumo to exorcise the Primordial Darkness from the player, and together they destroy the source of all evil in the universe once and for all, defeating Shiva in the process.
New Genesis Part One Prologue You land on the planet of Halpha in an escape pod and are awakened by Aina and Manon, residents of Aelio Town. Aina explains that those like you who land on the planet in escape pods are referred to as Meteorns and most are missing their memories. You fight through several mechanical enemies called "DOLLS" before meeting up with Aina's father, Garoa, and head to Aelio Town. Garoa teaches you how to use photons, a special energy source, to fight the DOLLS. After a short while, a large force of DOLLS attack. Garoa tries to fight the largest DOLL unit but is unable to damage it, and is seemingly killed along with everyone in Aelio Town except for you, Aina and Manon as Garoa orders you to flee to the caves.
Chapter One You head to Central City where you join the ARKS Defenders along with Aina and Manon. Crawford, the leader of the ARKS defenders, informs you that the large DOLLS unit that destroyed Aelio Town is called Dark Falz and they are preparing a plan to use a special cannon to defeat it as it is too heavily armored to defeat via conventional means, which is why Garoa was unable to damage it. Crawford has your group train with Instructor Dozer for a while, but Dozer's squad goes missing at a latter date. You rescue Dozer and help him defeat a powerful DOLLS unit, Nex Aelio.
Chapter Two Crawford sends you to the desert region of Retem to enlsit the help of the ARKS Defenders there in preparation for the battle against Dark Falz. Retem is plauged by constant attacks from DOLLS led by Renus Retem, and is unable to send help. Your group eventually helps Nadereh, the leader of the Retem ARKS to discover a special singing power which allows you to defeat the Renus Retem and it's army of DOLLS. Retem is now able to send troops to Central City.
Chapter Three Crawford sends you to the ice region of Kvaris to contact Illma, a researcher helping to work on the cannon that will be used to fight Dark Falz. You rescue Illma and defeat the DOLLS unit Ams Kvaris, allowing Illma to retrieve valuable research data from Kvaris's lost central city to help repair the cannon.
Chapter Four You are sent to the volcanic region of Stia to meet the ARKS Vanguard unit there, where they have discovered several bases producing DOLLS. You capture the bases and lure out Dark Falz whom was docked at one of the bases. Crawford orders a cannon strike on Dark Falz which damages it, forcing it to retreat. With the bases captured, Dark Falz cannot repair itself, and Crawford informs you that they will destroy Dark Falz the next time it appears.
Chapter Five You fight and destroy Dark Falz in the Central Region with the help of the cannon. Afterwards, Manon dissapears on her own without saying anything. A new Meteorn, Pharia, lands in Retem. She reveals that she knows that Manon went to Leciel, the floating structure above Halpha, which can only be accessed from a teleport in the Kvaris Lost Central ruins. You fight your way through Leciel to rescue Manon, who reveals that she knew the whole war between ARKS and DOLLS was Zephetto's experiment, and she was sent to Aelio Town to help gather data. In a way, she is responsible for Aelio Town's destruction and the death of Aina's father. But Aina forgives her and you press on to confront Zephetto, leader of the Resurgent ARKS, who reveals that the war between ARKS and DOLLS was a 300 year old experiment created to force ARKS to improve their photon sensitivity to fight the Starless, an unknown race that almost exterminated humanity 500 years ago. After the events of PSO2 1000 years ago, the long period of peace had caused their photon sensitivity to decline, preventing them from being able to fight against the Starless. Zephetto has been cloning ARKS defenders to send to Halpha as Meteorns to fight against the DOLLS to try and reclaim the power they had 1000 years ago during the events of PSO2. After defeating Zephetto, he is sastified that the experiment succeeded in raising the ARKS photon sensitivity to 100% just in time. However, the Starless chooses this moment to attack Halpha and Zephetto takes off in a giant mech to fight the Starless, leaving the future of humanity to the ARKS defenders on Halpha.
Part Two Chapter Six You are sent to investigate a scout team that has lost contact. While there, you are attacked by the Starless. After the battle, Crawford decides to make you a Guardian, a symbol of ARKS to increase morale. He also announces that they will be working together with the remaining members of Resurgent ARKS to fight the Starless. Aina becomes an instructor, while Manon becomes a researcher. Manon becomes sick with photon deficiency because she overused her Overboost power to help ARKS fight the dolls and everyone helps gather a rare medicine to heal her. You also help rescue Aina's training squad when they get ambushed by a large number of enemies.
Chapter Seven Zephetto takes control of Pharia temporarily and asks for help as he cannot move from his current location. He gives Pharia the information to get to the Resurgent ARKS headquarters which the other members of Resurgent ARKS do not know of. He specifically requests that You, Aina, Manon and Pharia alone head there. You head to the secret orbital facility that used to be the headquarters of Resurgent ARKS and find an abandoned city which they call the Nameless City where Zephetto possess Pharia again. He explains that Resurgent ARKS discovered a ARKS warrior in cold sleep from 1000 years ago, but were unable to thaw them as the pod was too heavily protected. They could only collect some genetic data from them and use it to make the first generation of ARKS. Zephetto is a surviving member of the first generation and his ability to transfer his conciousness was the product of experiments. Unfortunately, most of the first generation died because they could not withstand the genetic code that was injected to create the first generation and that most of the first generation died or became disabled. This caused a civil war to erupt in Resurgent ARKS as one faction no longer believed they were on the right path, and the pod containing the original ARKS warrior went missing and was assumed to have been destroyed in the conflict. He also reveals that test subject 909 from the third generation of ARKS was discovered to be in storage, and someone had switched out 909 with you before sending you to Halpha. He suspects that you are infact, the original ARKS warrior that was discovered to be in cold sleep from 1000 years ago. If you have obtained the final ending in PSO2, you will also see flashbacks of characters from PSO2, proving that your character in NGS is the same as the one in PSO2. The Starless begin attacking the orbital facility. After defeating some of the Starless, Zephetto shows you the 4th generation ARKS clone that was uploaded with all of your battle data, and that he will now transfer his soul to it as he lost his previous body defeating the Starless Vanguard at the end of Chapter Five. The Starless attack again, and you fight them off while Pharia helps to transfer Zephetto's soul to the clone. The transfer succeeds and Zephetto reveals that this body should have the power necessary to defeat the most dangerous Starless that destroyed the most planets in the war 500 years ago, and was also responsible for destroying Zephetto's anti starless squad and his home planet. However, something goes wrong and a Starless named Vael somehow manages to possess the clone body and use it to attack Aina. Zephetto manages to regain some control and stop Vael in time, and tells you to leave while he sends the body into space time. After returning to Halpha, Zephetto possess Pharia again and reveals that Dark Falz Vael is the leader of the Starless, and he barely managed to transfer a portion of his conciousness back into Pharia. While Vael will consume his soul soon, the fusion with Vael has revealed the truth of the Starless to Zephetto. The Starless have an insatiable hunger for Photons but found the ARKS members 500 years ago to have insufficient photons for their taste. Vael decided to hide himself inside of Zephetto and manipulate him for 500 years to increase the photon sensitivity of ARKS before starting the feeding cycle again, which is why the Starless suddenly stopped their attack 500 years ago. Zephetto believes Vael will soon complete his transformation using the power of the 4th generation clone and attack Halpha, but the current ARKS has the power to defeat him. After Zephetto's conciousness fades away, Pharia reveals that he told her how to fix the anti-Starless weapon that they have been working on. After some time, Vael is detected in orbit and you head to the Nameless City to fight it. You fight Vael and pursue it into space using the M.A.R.S, the special armament that Zephetto helped Pharia fix. After defeating Vael, he self destructs and the large explosions knocks you far off into space. Unable to get back to orbit, you are about to give up when you hear Zephetto's voice tell you that you will be needed in the future as his damaged mech appears behind you. You are sent flying back to the Nameless City where you land safely. While The Starless's leader, Vael, was defeated, the rest of the Starless still pose a threat but you resolve to continue fighting them.
Chapter Eight Crawford informs you that they have been exploring the Alter Realm that appeared one day, which is connected to Halpha via a dimensional rift. They lost all contact with the last research team. You search for the research team with Aina and Manon, but are find them fighting a mysterious woman. The research team attacks you as well and doesn't respond to attempts at communication. After fighting for a while, you are surrounded but the mysterious woman opens a dimensional rift back to Halpha, allowing all of you to escape. She reveals that she doesn't have any memories. After reporting the situation to Crawford, all of you decide to head back to the Alter Realm to investigate for further clues. Along the way, you encounter datapods left by the research team suggesting that they had found someone they knew and were attempting to track them. You lose communications with Crawford, but are contacted by a strange sounding Crawford afterwards urging you to head deeper into the Alter Realm. Eventually, Aina suggests calling the mysterious woman "Lucia" temporarily as she seems distressed by not being able to regain her memory. You discover that the Alter Realm is an alternate version of Halpha and includes the same terrain features as the original Halpha. You eventually discover the bodies of the research team and defeat a Starless ambush. Someone resembling Crawford appears, but Lucia reveals that he is a Starless and has the same feeling as the Starless you have fought up till now. The man calls himself "Alter Crawford", announces that the plan is proceeding but the time is not yet right, and leaves. ==Development==