Una colegiala llamada Natsumi Mizuki pierde un llavero de gatito que le regaló su madre cuando un policía cree que ella le tomó una foto dando información a los secuaces de la yakuza. Paul Wan, propietario del café Honky Tonk y amigo de los GetBackers, les da una conferencia a Ban y Ginji para que acepten el caso. Después de muchos planes fallidos, los GetBackers finalmente recuperan el objeto robado, pero Natsumi ha sido capturada por el policía y los secuaces de la yakuza. Los GetBackers corren a la escena, Ginji invoca un rayo de su cuerpo, parecido al de una anguila eléctrica. Luego, Ban lanza un agarre de doscientos kilogramos de fuerza. Una ilusión del mal de ojo de Ban hace que el policía sueñe con matar tanto a Ban como a Ginji, y luego ser asesinado a tiros por los policías. Después de que termina Evil Eye, a Natsumi se le devuelve su llavero. Luego,

Ban y Ginji están sin trabajo y se mueren de hambre. Sin embargo, un hombre sin hogar, llamado Yamamura, les da comida y refugio. Más tarde revela que solía ser dueño de una fábrica, pero su hija, Rika Yamamura, fue secuestrada debido a las continuas recesiones y la presión de los secuaces de la yakuza. Yamamura luego les pide a Ban y Ginji que recuperen a Rika de los secuaces de la yakuza. Después de que los GetBackers se infiltran en la mansión para salvarla, Rika los traiciona y admite que tiene todo lo que necesita de los secuaces de la yakuza. Sin embargo, los secuaces de la yakuza admiten que planeaban llevársela y obligar a su padre a venderla. Usando Evil Eye, Ban hace que Rika sueñe con el líder de los secuaces de la yakuza matando tanto a Ban como a Ginji, pero luego ve a los secuaces de la yakuza siendo quemados vivos. Una vez que ella se despierta, Ginji intenta convencer a Rika de que regrese con su padre, para su disgusto.

Hevn, un negociador, les cuenta a The GetBackers sobre un trabajo. Se encuentran con Haruo Ohtaki, quien les informa que recuperen la caja de un grupo llamado The Transporters. Ellos, a su vez, piden tener una parte de lo que hay dentro de la caja para aceptar el caso, que luego se supuso que era de platino. Los GetBackers se preparan para detener a The Transporters, pero pronto inician una persecución a alta velocidad. Mientras intentan acercarse al camión semirremolque, Himiko Kudo rocía un perfume venenoso sobre Ginji, dándole la mente de un simio por un corto tiempo. Esto, a su vez, hace que Ban pierda el control, enviándolos por un precipicio. Mientras The GetBackers busca a The Transporters, Ban le recuerda a Ginji sobre Himiko y cómo obtuvo el apodo de "Lady Poison". Luego, los transportadores son bloqueados por un interceptor y su pandilla. Sin embargo, Kuroudo Akabane, mata al interceptor y su banda sin ayuda de nadie.

Mientras los GetBackers se preparan para luchar contra los Transportadores, Ginji planea luchar contra Akabane, mientras que Ban planea recuperar la caja. No mucho después, los GetBackers están en un aprieto cuando Akabane intenta dividir a Ginji. Ban se rinde y Ginji es capturado por los Transportadores. En el camión semirremolque, Ginji y Himiko conversan sobre Ban. Himiko recuerda su tiempo con Ban y su hermano mayor, Yamato, como antiguo servicio de recuperación. Sin embargo, Himiko lamenta haber conocido a Ban, ya que él fue el responsable de la muerte de Yamato, pero Ginji afirma que cree en Ban. Ban alcanza a The Transporters para rescatar a Ginji. Usando el mal de ojo, Ban rescata a Ginji y recupera la caja. Luego, los Transportadores planean su próximo ataque a GetBackers con Himiko explicando a Akabane que el mal de ojo solo se puede usar tres veces en una persona en un solo día.

Los Transporters se enfrentan a The GetBackers en un santuario abandonado. Ginji y Akabane luchan mientras Himiko y Ban luchan. Ban sorprende a Himiko con su agarre, derrotándola, antes de que casi le cuente sobre la muerte de Yamato. Akabane muestra el alcance de sus cuchillos brillantes, pero Ginji los manipula con electricidad magnética, derrotándolo. Ban y Ginji abandonan el santuario para reanudar su recuperación. A la mañana siguiente, Himiko quiere encontrar a los GetBackers, pero Akabane afirma que se ha divertido más que suficiente con ellos por el momento. Cuando Akabane abandona el santuario por su cuenta, Himiko y el conductor Maguruma encuentran a los GetBackers. Mientras Maguruma se prepara para embestir a los GetBackers de frente, Ban usa Evil Eye en un cuervo cercano, lo que hace que sueñe con muchos cuervos atacando el camión semirremolque, lo que luego hace que Maguruma se estrelle contra un poste.

Una violinista ciega y prodigiosa, llamada Madoka Otowa, y su perro guía, llamado Mozart, son acosados ​​por un grupo de matones callejeros. Ginji llega para salvar a Madoka y Mozart, pero todos se encuentran con Kazuki Fuchouin, un ex miembro de VOLTS dirigido por Ginji. Ginji y Madoka se dirigen al café Honky Tonk, donde se les pide a los GetBackers que recuperen un violín Stradivarius de manos de Shunsuke Akutsu, un violinista de renombre mundial. Deben obtener este violín antes de la actuación de Madoka la noche siguiente. Los GetBackers, incluidos Paul, Hevn y Natsumi, llegan disfrazados de músicos a la propiedad de Akutsu. Shido Fuyuki, otro ex miembro de The VOLTS que ahora trabaja para Akutsu, recibe la orden de acabar con los GetBackers. Planean su próximo movimiento, solo para caer en la trampa de Akutsu. Mientras tanto, Mientras Madoka busca en la finca su violín Stradivarius entre muchos violines, se encuentra con Shido, quien la perdona.

Justo cuando Ban intenta matar a Shido con su agarre, Kazuki llega para ayudar a Shido. Ban escapa cuando Ginji, Hevn y Madoka se encuentran con un Protector, llamado Ryuudou Hishiki. Ginji luego crea un corte de energía en la finca. Ban se encuentra con Paul y Natsumi, y Ginji, Hevn y Madoka encuentran a Akutsu y el Stradivarius. Akutsu le devuelve el Stradivarius, pero después de que se van, Akutsu le ordena a Kazuma Kurobe, uno de sus hombres, que entierre a Madoka con su violín en la finca. El grupo de Ginji se encuentra con el grupo de Ban y escapa de la finca, y Sugahara, el guardián de Madoka, llega justo a tiempo. Deja a Ban y Ginji en la carretera y se revela como Tsujima Kurobe, el hermano menor de Kazuma Kurobe.

Ginji se electriza, sorprendiendo a Hishiki hasta dejarlo inconsciente. Ginji se disculpa con Ban por hacer que Shido atacara al grupo, ya que se culpa a sí mismo por abandonar a Shido. Mientras Ban y Ginji intentan encontrar a Shido, Hevn y Madoka también ayudan. Ginji intenta ayudar a Shido, quien le pide que pelee solo. Después de derrotar a Kurobe, Shibo ordena discretamente a Mozart que robe el violín Stradivarius y lo devuelva a la finca. Madoka, a su vez, dice que se permitirá tocar un violín normal durante su actuación por la noche. Más tarde, Shido le devuelve el Stradivarius a Madoka. A cambio, Madoka se ofrece a actuar para Shido en las calles por la tarde, atrayendo a Visconti, el profesor de violín de Madoka. Visconti luego complementa su actuación con los demás, notando en broma que Madoka está enamorada de Shido.

Los GetBackers son llevados a la galería de arte de Clayman, donde se exhiben muchas obras maestras. Clayman se ofrece a ser un cliente de "reemplazo" de The GetBackers, ya que Ban y Ginji estaban asombrados con todas las obras maestras mostradas. Clayman explica que se convirtió en una ladrona de arte para proteger las obras maestras de los llamados "estafadores". Hachisu y el equipo SWAT hacen una aparición repentina, ya que Hachisu señala que usó The GetBackers para ubicar la galería de arte de Clayman. Admite además que la decimotercera pintura de Sunflowers era de hecho una falsificación. Ban usa su mal de ojo en Hachisu, lo que le hace soñar con quemar inesperadamente todas las pinturas hasta convertirlas en cenizas. Hachisu y Abukawa asisten a una reunión de negocios al día siguiente. Ban y Ginji llegan y recuperan la decimotercera pintura de Sunflowers, confundiendo a Hachisu.

Hevn contrata a Ban, Ginji, Shido, Kazuki, Akabane y Himiko para trabajar en equipo. Los llevan a un edificio abandonado cerca de Limitless Fortress, un lugar familiar para Ginji, Shido y Kazuki. Cuando entran, Hevn presenta al equipo a un grupo de hombres enmascarados con trajes. El líder de los hombres enmascarados informa al equipo que recupere algo del interior de la Fortaleza Ilimitada, apodada el nombre IL. Luego, el edificio se autodestruye repentinamente, cuando el equipo se marcha. Deciden comenzar la tarea al día siguiente. Por la mañana, el equipo se dirige a la Fortaleza ilimitada. El equipo se separa de Hevn, pero pronto es secuestrada. Mientras tanto, el equipo lucha contra más hombres modificados y luego se familiarizan con Shuu, un ex miembro de The VOLTS. Kumon Horii luego mata instantáneamente a Shuu y rocía un gas venenoso alrededor del equipo. Esto hace que Ginji se enfurezca, sin embargo, se ve afectado por el gas venenoso.

Akabane waits for Ginji to wake up after being unconscious from the effects of Horii's poisonous gas. Akabane tells Ginji that the rest of the team went out to search for the IL, which upsets Ginji. Meanwhile, Ban and Shido are in another route in the Limitless Fortress, as Ryouma Magami and Ayame Magami, two former members of The VOLTS, show up to face off against them. Ban and Shido notice that Ryouma and Ayame modify their body as their weapon source. Ayame leads Ban into a trap door. The lights are turned on to revealed that the basement is really an abandoned laboratory. He reveals that he has imprisoned innocent women, who he plans to modify as well. Ban chants an incantation, increase his strength and gripping power, releasing himself from the trap. He then goes berserk on Ayame, destroying his modified body. He frees the women and finds a way out from the laboratory. Meanwhile, Shido defeats Ryouma. Ban meets up with Shido, frustrated to know about body modification on innocent people. After discussing, Ban and Shido believe that Makubex, the youngest Four King who was born in the Fortress, is responsible.

As Makubex spyes the recovery team with cameras, Himiko and Kazuki are fighting off several men. Kazuki reveals himself to Himiko to be the traitor in the team, as he wraps her up in threads. However, the real Kazuki shows up to announce that the other "Kazuki" is an impostor. The impostor removes his mask, revealing himself to be Kogenta Akame, a student of the West Fuchouin-School. Kazuki and Akame then engage in a thread technique battle. Kazuki defeats Akame and saves Himiko. However, Himiko becomes unknowingly controlled by Makubex, by a wire from his computer to Himiko's body. As Kazuki figures this out, he attempts to cut the wire, but is stopped by Juubei Kakei, an assistant of Makubex, who throws him needles. Juubei chases him, but Kazuki causes an explosion and escapes. Makubex commands Juubei to bring Himiko, now unconscious, to him. Makubex then plans out his next move, as Takuma Fudou brings him the kidnapped Hevn, which he might use her as a hostage.

Ginji sees an image of himself when he was younger, and goes berserk when Akabane kills it. Akabane then sees multiple copies of Ginji, later revealed as projections, and he easily defeats them, as the real one calms down. Ren Radou, a pharmacist, takes Kazuki to a pharmacy. Gen Radou, Ren's grandfather, also checks up on Kazuki. As Kazuki leaves the pharmacy, Gen tells him that Makubex wants to live in a world of suspicion, where people will fear betrayal. Hevn and Himiko are imprisoned in chains in a jail cell. Two men, jeering at them, walk in to harass them. Himiko sprays poisonous perfume, to control the minds of the two men, telling them to unshackle the chains. Hevn and Himiko look for the rest of the team. Kazuki, Gen, Ren try to figure out where Makubex is hidden. Smelling Himiko's perfume, Ban deducts that Makubex and supposedly the IL are in the garbage disposal facility. Once they've figure that out, they are attacked by several men, controlled by Makubex's wire doll system. Fudou shows up and engages Ban in battle, seeking to kill him. Haruki Emishi, a former member of The VOLTS, makes a surprise entrance, which results in Fudou escaping.

Emishi takes Ban and Shido to his safe house where Ban gets acquainted with many girls residing there. Later, Emishi attacks Shido with his Loulan Death Whip, making him unconscious. Inside, Emishi undoubtedly uses his whip to attack Ban, but Emishi hallucinates. Ban reveals to Shido that he used Evil Eye right when Emishi first appeared, realizing he was a soldier from Makubex due to Fudou's sudden escape. Afterward, Ban and Emishi engage in battle, as Shido join in as well, but Emishi then escape. Ban and Shido, as well as Kazuki, Gen, and Ren find out that the IL is an implosion lens, used as an atomic bomb. Ban and Shido unwillingly fights off more men controlled by the wire doll system. As Kazuki departs from the pharmacy, it is revealed that Gen is working for Makubex as well. Meanwhile, Ginji tries to escape from Akabane, but is he caught up, Akabane finds out that the IL is located in the garbage disposal facility.

Ginji and Akabane battle against several men, but Ginji disagrees with Akabane ruthless attacks. Kagami sets out to look for Ginji and Akabane, while Juubei follows him. Makubex reveals how the Limitless Fortress is divided into three sections: Lower Town, The Beltline, and Babylon City. His objective therefore is to obtain absolute power from Lower Town. Juubei and Kagami encounter Ginji and Akabane, but Ginji is enraged when Juubei tells him he killed Kazuki. Ginji unleashes a huge amount of lightning, which both exhausts them as well as separates them. Akabane and Kagami also engage in battle, with Akabane forcing Kagami to escape. Juubei raises doubts about Makubex, but Kagami advises him to continue the path he chose. Ban and Shido manage to find the garbage disposal facility. Meanwhile, as Hevn and Himiko are harassed by two men, Kazuki saves them.

As Makubex plans out the next move, Fudou becomes impatient with him, longing to have another battle with Ban; kazuki, Himiko, and Hevn face children under the wire doll system. Reluctantly, Ginji and Akabane are able to stop the children. The five of them come a circular room, where Ban and Shido also arrive calming Fudou. Once they reunite, it is revealed that Gen and Ren witness the room where the seven of them are in. It is also revealed that Gen is the architect of Babylon City. In the circular room, there are six numbered doors. Ginji finds a die and gives the idea that everyone, except Hevn, take turns rolling the die, and each person would go to their numbered doors, based on the number rolled. Akabane faces off against Makubex. Meanwhile, it first appears that Kazuki and Emishi are to battle, but Shido and Juubei come to their respective support.

It is revealed that the four will fight on the Grand Canyon as their battlefield. After one hit from his whip, Shido begins to seriously focus on the match with Emishi. Emishi admits that he would loses against Shido in a match, but he truly wants to fight Shido regardless, as Makubex is protecting his clan. Emishi creates an explosion of flames, yet Shido is able to save him at the last second. Shido tells Kazuki that he will take Emishi to see Gen and Ren. It is revealed that the Grand Canyon battlefield is a virtual reality room, exposing its illusion. Kazuki starts out strong using his thread technique abilities, but Juubei struggles as he fights back with his flying needles technique abilities.

At the Honky Tonk cafe, an informant asks about the whereabouts of Ginji. Paul and Natsumi says that he is with the GetBackers in the Limitless Fortress. Meanwhile at the Grand Canyon, Juubei presents the black needles, which is a forbidden technique. Kazuki get stung by them, and then he figures out that the black needles are magnetic, controlled by a black ore stone. However, using the black needle will gradually drain the energy of Juubei. Juubei attacks at full force, but Kazuki manages to defend, causing a whirlwind of threads and needles. In a flashblack, it shows when Juubei first met Kazuki as the former's clan has been protecting the latter's. After the West Fuchouin-School was burned down, Kazuki and Juubei were told to go to the Limitless Fortress to live. Juubei remembered that Makubex believes that everything that is happening in the Limitless Fortress is caused by the people of Babylon City. Hevn and Shido arrive at the pharmacy, noticing that Gen is witnessing the battles. Kazuki and Juubei continue their fight, white threads against black needles. Juubei is caught is one of Kazuki attacks, urging him to give up. He then stabs himself using the black needles, causing Kazuki to wail. Kazuki carries Juubei out of the virtual reality room.

Akabane reveals his transporting assignment to give Makubex a box of plutonium. And he then says that he still has a recovery assignment to retrieve the IL, keeping the promise to both clients. Watching from the pharmacy, Hevn and Shido see that Himiko is up against Kagami, having faith in her victory. It is then seen that Himiko and Kagami will fight in the Mayan Temple as their battlefield. As he reveals himself, he outsmarts her with his mirror fragments, to gain the upper hand. The sacrificial ritual begins, as Himiko lies at the altar of the temple. Suddenly, Himiko and Kagami switch places, causing him to be "sacrificed". However, Ban reveals himself, as he has used Evil Eye on Kagami before Himiko was sacrificed. Himiko and Kagami resume their battle, as Ban watches. Himiko uses her poisonous perfume to increase her speed, catching Kagami off guard. Ban joins in the fight and the two use their supersonic speed to attack Kagami. Kagami later retreats as the objective is to protect the IL. Himiko becomes exhausted from using the poisonous perfume, as it begins to drain her energy. Ban helps her recover, then leaves her in the virtual reality room. Ban goes to another virtual reality room to face off against Fudou.

Fudou says that he wants Ban to feels limitless pain and suffering as a way to avenge the loss of his real arm. The battlefield where hey will be face off is in the Roman Coliseum. As Gen and the others witness this battle, Kazuki comes in the pharmacy carrying Juubei. Ginji finds himself in the ruins of the Limitless Fortress and sees Shuu, who was supposedly killed before. Suddenly, all the children turn into zombies, frightening Ginji to the point of killing them. Then he encounters Takeru Teshimine, the informant who visited the Honky Tonk cafe. Teshimine recalls to when Ginji first made friends when he was younger, seemingly abandoning Teshimine. He then says that Ginji witnessed all his friends be slaughtered, blaming Ginji for this. A enraged Ginji begins transforming into the Lightning Emperor once more. Teshimine reminisces to when Ginji first transformed into the Lightning Emperor, and then he admits that he wanted to raise Ginji to gain his immense power to rule over the Limitless Fortress. Teshimine causes Ginji to unleash huge amounts of lightning, affecting the Limitless Fortress entirely. At the pharmacy, Shido prepares to depart with Hevn in order to stop Ginji's reckless behavior. Fudou seems to have gained the upper hand, as Ban is losing his strength and speed. Ginji's lightning causes the illusion of the Roman Coliseum to disappear. As Ban yet again recites an incantation, he uses his grip to destroy Fudou's metallic arm, attempting to find and stop Ginji.

It is revealed that Teshimine was an illusion to Ginji, as the real Teshimine is still in the Honky Tonk cafe. Ginji finds Sakura, and then injures her with his lightning. As Akabane enters, Ginji is caught off guard. As Ginji uses his lightning to attack, Akabane evades each attack with his supersonic speed. A power outage occurs in Lower Town, and Kazuki and Emishi are forced to leave Gen and Ren in the pharmacy. As the two participate in hand-to-hand combat, Ban steps in, disrupting the battle and seeming has been killed. However, Ban tells he used the Evil Eye on Ginji to fake his death, surprising Ginji and changing him back to normal. At the Honky Tonk cafe, Teshimine prepares to leave, with Paul and Natsumi asking him to come back anytime. Makubex attempts to install the IL, but the computer system has been jammed by Gen's doing. Gen reveals to Ren that he was responsible for teaching Makubex the basics of computer programming, as he was able to learn very quickly. Makubex download an intruder interception program to supposedly attempt to reinstall the IL without fail. Nonetheless, this will slow down his operation. Akabane admits that he transported the box of plutonium to Makubex, making Ban and Ginji feel betrayed. As Akabane takes Ginji with him to recover the IL, it is revealed Ban faked his Evil Eye and encounters a seemingly revived Fudou.

Fudou attacks Ban head-on, but Shido manages to come just in time to save him. All of a sudden, multiple clones of Fudou appear out of nowhere in front of Shido, and multiple clones of Akabane appear out of nowhere in front of Ginji and Akabane. As the Fudou clones begin to attack, Kazuki and Emishi step in, as they figure out that the intruder interception programs creates clones based on collected data. As Akabane fights off the Akabane clones, Ginji meets up with Ban and Hevn, and the four of them proceed to stop Makubex. Sakura wakes up only to find herself in the pharmacy. Himiko tells her that she was the one who brought her there. Juubei, blinded by his black needles, tells Sakura that Makubex made a mistake in his calculations. Sakura tells Gen that Makubex obtained his data by hacking into the mainframe of Babylon City, as well as for the virtual reality technology. Gen reveals that he was the one who raised Makubex. Juubei wants to leave with Sakura to help stop Makubex, while Himiko tags along as well. Meanwhile, after Shido, Kazuki, and Emishi finish off the Fudou clones, clones of themselves appear. Elsewhere, Ban, Ginji, Akabane, and Hevn encounter Kagami. Shido, Kazuki, and Emishi manages to catch up with the other four. Kagami lets the seven of them pass to see Makubex, who happens to be expecting them.

Ginji pleads with Makubex to give back the IL to the GetBackers, but to no avail. After confrontation with Makubex fails, Ginji volunteering to fight him face-to-face. Ginji attempts to attack him head-on, but Makubex deflects his attack, electrocuting the other six. Then Makubex "transforms" the room into the inside of his body, which appears to be an illusion. He proves the illusion as reality, which confuses them. Ginji deducts that Makubex is suffering, and then asks him to fight in order to help him. As Ginji and Makubex continue their battle, the others realize that these two are evenly matched in strength and ability. Ban wonders if the Limitless Fortress is in itself a virtual reality, as they have witnessed injuries healing rapidly and strength increasing immensely. Through a flashback, it is revealed that Ban suggested Ginji to join up with him, due to Ginji uncertainty of remaining with the VOLTS due to his growth in powers as the Lightning Lord. As Ginji delivers the final blow toward Makubex, it seems that Makubex and the inside of his body was all just an illusion, as he used this illusion to buy time in order to install the IL completely into the mainframe of the computer system.

With the intruder interception program active, none of GetBackers there can stop Makubex. Makubex says that he was aware why Ginji left the Limitless Fortress in the first place. He mentions that he hacked into the Babylon City database and found an information storehouse called the Archive, a prophecy foretelling the future of the Limitless Fortress. Makubex wanted the IL to serve as a way to break the bonds from Babylon City, and to create a "new" Limitless Fortress. As the team try to stop him, Makubex finds himself in an illusive world. Mabukex witnesses the result of his profound utopia, as well as the absence of The VOLTS. He then sees a reflection of himself announcing he will the return of the world to nothingness and detonating the IL, consequently resulting in the ruins of the Limitless Fortress, as Makubex turns into ashes. However, Ban reveals using Jagan on Makubex. Ban destroys the detonator, and Makubex evades the team, locking them in the computer system room. Ginji uses his lightning to break open the door. As he leaves, Emishi tells him that Makubex turned into a hardhearted person for the sake of The VOLTS disbanded. Makubex attempts to commit suicide, to find out whether he himself is real or fake. As he falls, Ginji breaks through a window, and saves him. Ginji tells Makubex that his death would surely affect those around him, saying that there are many who love and cherish him. Makubex cries tears of joy as he reunites with everyone, changing him back to his warmhearted self. He vows to protect those he loves and to see the error of his ways, announcing the new formation of The VOLTS. He gives the IL, mentioned as a file stored in a floppy disk, back to The GetBackers. The GetBackers return the IL to the masked men, who are killed by Akabane when they try to kill them. The team part ways, and Ban and Ginji return to the Honky Tonk cafe.