In an unnamed country, Hyōbu surrenders to the military and is sent to a special esper prison. Upon his arrival, Hyōbu meets Andy Hinomiya, an esper prisoner who somehow does not any apparent powers. After creating some commotion, both are sent to confinement where Hyōbu offers Andy a chance to join his side, which he accepts upon helping him escape the prison. During meal time, the cooks put some drug on Hyōbu's drink but he gives it to Andy instead, knocking him unconscious. Andy wakes up in a surgery room outside the prison and is freed by Hyōbu, who explains him that the prison is being used as a site for illegal esper experiments. Together, they reach the place where a young esper child, Yūgiri is being held. The prison warden sends a monster created by fusing several esper body parts to attack them, but it ends up being destroyed when Hyōbu deactivates his own limiter, unlocking his true power. In the end, Hyōbu, Andy and Yūgiri are picked up by the other members of P.A.N.D.R.A.

A week has passed since USEI Investigator Hinomiya has boarded PANDRA's ship, 'Catastrophe.' The crew learns of his ability to negate all ESP abilities, and that ESP users near him may produce symptoms such headaches, dizziness, or toothaches. Magi is suspicious of Hinomiya due to issues with Hinomiya's past; even moreso that they cannot read his mind with ESP. PANDRA is to make a trade, smuggling weapons, with a certain mafia boss, Carlo, who is a friend of Hyobu's from WW2. Hyobu is actually very old, but he uses his ESP abilities to regenerate himself to keep his youth. Shortly after arriving, PANDRA is attacked by the mafia they were to trade with. Despite this, Hyobu insists on visting Carlo. He gives orders to Hinomiya to shoot Carlo if he gives the signal, but upon giving the signal he is unable to shoot. Having already calculated this, Hyobu uncovered his disguised clones and kills Carlo, whom was actually a robotic decoy.

Minamoto and Sakaki attend a party held by the Princess of Monarch, Sophie Grace for esper organizations from several countries where they spot Hyōbu and some members of P.A.N.D.R.A. After being confronted by the duo, Hyōbu and his party flee undetected and some time later, it is revealed that Sophie is also missing. While Sakaki and Minamoto inquire the authorities and try to access the contents of a USB flash drive Sakaki snatched from Hyōbu's pocket, Sophie is seen under custody of P.A.N.D.R.A., but it is revealed that it is part of their plan to protect the princess from an assassination plot by Yūgiri's request. As Sophie befriends Yūgiri and decides to take her for a walk around the city while escorted by Andy, Hyōbu makes use of mass hypnosis to have all women in the country seen by all around her as the princess, while feeding their enemies with false info about her whereabouts to lure them to a trap.

As the Catastrophe approaches the coast of Japan, Andy is searching the ship under his superior's orders when it is attacked by the members of B.A.B.E.L. who send "The Children" to infiltrate it. Hyōbu confronts Kaoru by himself while Andy is detained by Aoi and Shiho who steal the ship's master key from Momotarô and use it to hack the Catastrophe's main computer. Once regrouped, the members of P.A.N.D.R.A. start a counterattack with Andy subduing Fujiko with his second esper power, the ability to neutralize temporarily the powers of someone he touches and destroying the hack's control while the rest of the group distracts The Children. In a last effort to capture the Catastrophe, Kaoru, Aoi and Shiho combine their powers with their limiters' "Triple Boost" feature to restrain it, but they are repelled by Hyōbu when he unlocks his own limiter, giving them the chance to escape.

As the Catastrophe is undergoing repairs after their clash with The Children, Andy is tasked by Magi, Momiji and Yoh to accompany Yūgiri as they are summoned back. Meanwhile, Hyōbu infiltrates a B.A.B.E.L. medical facility to perform some exams on his body in secret. While taking Yūgiri to an amusement park, Andy is approached by Minamoto and Fujiko who reveal to him that they know he is a spy under the US government infiltrated on P.A.N.D.R.A. and ask for his cooperation to apprehend them as Sakaki keeps watching Yūgiri, who is exposed as an esper after she uses her powers to help a lost boy. Feeling herself rejected by those arround her, a desperate Yūgiri loses control over her powers, igniting a disastrous hypnotic trance that is contained when Andy comes to help her. Soon after their companions appear and bring them to safety.

As Andy reminisces about when he was recruited by the US government, he is informed by his superiors that the time has come for him to finish his assignment. Hyōbu informs the others that their next mission is to steal a new ECM device developed in the United States. Andy then relays the info about the mission to B.A.B.E.L. who agree to set a trap to P.A.N.D.R.A., although they decide to not take The Children with them this time, despite Kaoru's protests. With Hyōbu and the others cornered by Minamoto's team, Andy takes the opportunity to return to the Catastrophe and accomplish his own mission, which is to extract the ship's main defense system, "Ihachigo". Hyōbu follows soon after, but is halted by Kaoru who had just learned about a precognition regading an impending destruction of the Catastrophe. With his body showing signs of fatigue, Hyōbu goes full force against Kaoru, knocking her unconscious and finds Andy as he reaches Ihachigo's chambers.

Several decades ago, a young Hyōbu who had recently lost his father moves to live with Fujiko and her father in Japan. Some time later, both Fujiko and Hyōbu are asked by Captain Eiji Saotome to join a new Esper special unit created under the Japanese Army. Fujiko declines despite Eiji's claim that the unit's purpose is not to help with Japan's invasion of other nations but to help with the country's defense, in spite of a similar initiative in development by the Third Reich, while Hyōbu was instructed by his late father to refrain from using his powers to avoid being used as a living weapon. However, some time later, both Hyōbu and Fujiko accept the offer and join the Army.

Eiji chooses Hyōbu to represent the ESP unit in the duel with the navy fighter, but the words of his father that he should refrain from using his powers keep haunting him as he trains for the upcoming match. In the day of the duel, it is revealed that the pilot representing the navy is the same one involved in the incident. Hyōbu finds himself in a pinch against the enemy until he finally manages to overcomes his fear and wins the duel by a direct paint shot in the cockpit. Soon after, a US submarine is seen pursuing three dolphins who contact Hyōbu and the others through ESP asking for their help, just before one of the dolphins is killed by a torpedo. With the navy fighter's help, the ESP unit manage to save the other two and shake off the pursuers. However, the dolphins warn Hyōbu about an ominous fate awaiting him and his companions. Years later, just after the atomic bombing of Hiroshima, Eiji informs Hyōbu that Japan is about to surrender and most of the ESP unit is dead.

Back to the present, Andy uses his powers to deactivate Ihachigo's cloaking system, exposing the Catastrophe to an attack by the US military. While confronting Magi and the others, Minamoto learns about the situation, and reveals that B.A.B.E.L.'s true intention was to aprehend P.A.N.D.R.A. to prevent the attack and allows them to leave and help Hyōbu and the others. With Hyōbu busy confronting dozens of combat drones sent by the US army, a task force invades the ship and captures Yūgiri. Andy tries to stop them from taking her away, but his superior shoots him instead and leaves with both Yūgiri and Ihachigo in his possession. Andy awakens soon after, just to find he is unscatched as his limiter stoped the bullet.

Andy saves Hyōbu from drowning and the two are rescued by B.A.B.E.L.. Fujiko and Sakaki take Hyōbu to the Tsubomi Estate to treat him, while Oboro has the transmitter chip from the US extracted from Andy's body and destroyed with The Children's help. By Kaoru's request, Shiho restrains Oboru and learns Hyōbu's location from her. Andy convinces the girls to take him with them, and upon arriving at the mansion, Hyōbu asks him about the man who contacted them aboard the Catastrophe, confirming his suspicions that said man is none other than Eiji Saotome himself who somehow is still alive. Meanwhile Sakaki reveals to the girls that Hyōbu is dying and to save his life, Kaoru offers herself for a blood transfusion. Now in possession of both Yūgiri and Ihachigo, Eiji plans to use both to avert the Esper Revolution led by Kaoru and Hyōbu set to occur in the near future.

Upon arriving at home, Andy's former contact in the USEI is held into custody by him with Hyōbu's help and is forced to take them to the facility where Yūgiri is being held. However, the agent manages to warn his companions about them in secret and the two arrive there just to find that Yūgiri is not there anymore and after a brief conversation with Eiji, who reveals to them his intention to use her to kill Kaoru, the two find themselves in an ambush. Andy and Hyōbu fight to escape until they are cornered by the enemy, just to be rescued in time by Magi and the others. Once again reunited, the members of P.A.N.D.R.A. set to New York, as Hyōbu realizes that Eiji's next target is Norman Green, the newly elected mayor who is a supporter of esper-protection policies. Somehow put under some kind of trance, Yūgiri defeats Magi, Momiji and Yoh before she comes across Andy.

Andy follows Yūgiri to the site of Green's inauguration but is restrained by the police, just to be rescued by Minamoto and Sakaki, who reveal to him that they are working with Liberty Bell to stop Eiji's conspiracy to have the new mayor assassinated by an esper and alter the future. Yūgiri attacks Green, just to be stopped by Andy, and she launches a hypnotic trance that afflicts everyone in the area except Andy and his allies, starting a riot. As the riot spreads through the city, Hyōbu confronts Yūgiri to free her mind, but her hypnosis makes him confront delusions of his past, until he unlocks his powers knowing that with his body's condition, this may end up killing him. Hyōbu succeeds to rescue Yūgiri, but his powers go haywire and he asks Andy to take her away before they destroy him. However, Andy refuses to flee and uses his ability to restrain Hyōbu's powers and save his life. As the members of B.A.B.E.L.