Galactor has a spy infiltrate a passenger ship with a lot of ISO engineers onboard. He attaches a homing system to the ship and it is then blown up by firing torpedos into it.
Nambu, afraid that such a incident may happen again, sends the Science Ninja Team on a patrol. The God Phoenix dives at the spot where the ship sank and encounters crab-shaped tanks. Seizing the opportunity when the Science Ninja Team is distracted by the tanks, a submarine attaches itself to the belly of the God Phoenix. When the crab-shaped tanks are sure of this, they retreat. The Science Ninja Team doesn't trust this move, but they nevertheless go back to their base when Nambu orders them to do so. The Galactor submarine manages to easily sneak into Crescent Coral. The crew kills some engineers disguise themselves and install the homing system in the base.
The assaulted engineers are discovered and Nambu suspects that a homing system equal to that in the passenger ship has been installed. He orders Ken and Jun to find the system, and Joe and the rest to find the submarine which fires the torpedos.
Ken and Jun search the interior of the base, discover the Galactor members disguised as engineers and corner them. However, the Galactor members press a button, per Katse's instructions, which causes the submarine to blow up completely. Thus destroying the one clue as to the location of the tracking device. It's nearly impossible to search the huge base with its complicated layout.
Elsewhere, the God Phoenix is searching the bottom of the sea, but it cannot detect the submarine which hides close by.
Convinced of his victory, Katse's laughter resounds as torpedoes are launched towards Crescent Coral.
One after the other, the torpedoes hit right on target.The props of the camouflaging coral reef get stuck in the base which loses its balances and starts sinking towards the bottom of the sea.Inside, the engineers don't want to just leave their research, but Ken and Jun convince them the really important thing is their lives. They make them escape. Meanwhile, while Nambu is destroying the data a big computer falls over and traps his leg, rendering him immobile.
The God Phoenix notices the sound of the explosions and returns to the base. After making sure of this, another group of torpedoes attacks the base. Overturning, the base is caught on the wall of a deep-sea trench and the God Phoenix cannot escape from the hangar. Ken and Jun have managed to arrive at Nambu's room, but they can't open the door because the electrical system has been shut off. They sit down, awaiting their last hour. However, the base starts falling towards the deep-sea trench again and through this shock, the God Phoenix tears down the hangar's shutter and breaks into the interior. Joe and Jinpei go to Nambu's room, crossing flooded areas. They meet with Ken and Jun. With the burner in Joe's airgun they break open the door and rescue Nambu. The God Phoenix separates itself from the sinking base. The Science Ninja Team watches for a long time how the form of the own base sinks deep into the deep-sea trench. Nambu orders them to blast the base. When he tells them that it would be easy for Galactor to save data from the base in the deep-sea trench, Ken presses the firing button for the Bird Missiles.
The basis of the Science Ninja Team, Crescent Coral, has ceased to exist.
Katse is happy that he has defeated the Science Ninja Team. An order comes in from X to make sure that the Science Ninja Team is dead.
Meanwhile, the Science Ninja Team spends its days at Nambu's villa. Without means to do anything after the heavy blow of losing the base, the data of the Mantel plan, and a place to produce missiles. Then the message is received that a tourist city without any strategic value has been attacked. The Science Ninja Team wants to get mobilized, but Nambu stops them and leaves the field to the UN troups.
Despite the attack on the city, the Science Ninja Team does not appear. Katse is convinced that the Team is dead and proceeds to his operation of destroying UN bases and factories with subterranean torpedoes.
Based on the destroyed locations, Nambu derives where the torpedoes were launched from and sends the Science Ninja Team there. The Ninja Team sneaks into the base and discovers there a storage room for the torpedoes. Joe collects everybody's small detectors and installs them on the torpedoes.
During the celebration for the destruction of the Science Ninja Team, Katse is in the middle of a speech with a tape in his hand that came in with X's latest plan for conquest. Katse and the Galactor members are startled by the Science Ninja Team appearing there. Seizing the opportunity, they grab the tape. Katse orders the torpedoes launched and the base destroyed, then flees from the base.
The God Phoenix follows the mecha and fires the last Bird Missile. A transmitter has been installed in the missile and the torpodoes go one after the other in direction of the mecha.
They bring the tape back to Nambu, but when they try to play it, it disintegrates in a column of white smoke.
The Torasshuu power plant provides electrical power to the city of Utoland. Nambu charges its head, Dr. Komibe, with the testing whether a space capsule is fireproof or not. A test which requires the highly powerful incinerator of the plant.
That evening, Ken and the others come to the station to say goodbye to Ryu, who is boarding the night train because his father is in critical condition. However, while Joe is heading towards the station, he hits a child and brings it and its mother, to the hospital.
During a testflight for the mecha Angler, Katse lands by the power plant and forces them to recharge the mecha. This causes a blackout in the city. As a result, Ryu expects the re-establishment of power supply in the middle of the train, Joe in the hospital, where they are in the middle of the operation, the other three in a restaurant. But Ken and the others get suspicous at the length of the blackout. They go to the power plant. Katse, disguised as Komibe, throws the three of them into the incinerator and installs a pendant bomb inside the plant.
The incinerator is fired up, but by fleeing into the capsule left by Nambu, they escape from the danger. They defeat the Galactor members who come to check on the situation. Jun then plans, with the help of Komibe, the re-establishment of the power supply and Ken attaches the pendant bomb discovered by Jinpei to his boomerang and throws it after the fleeing mecha.
When Katse wants to blow up the power plant and presses the button, the mecha itself explodes.
The power comes back to Utoland City. Ryu learns on the phone in the train that his father has overcome the critical condition. In the hospital, Joe is relieved by the fact that the operation on the child was a success.
In the Jupiter mountains, there are ruins of a fortress which is said to have been erected by ninjas of ancient times. There some strange corpses are found. Nambu charges Jun, who is familiar with this region, with the investigation.
Jun has found Jinpei in the Jupiter mountains. It was decided that this day would be Jinpei's birthday and it has been celebrated ever since. Despite that, Jinpei is in a bad mood that Jun has gone away this year because of the investigation. Ryu tells him that, since he doesn't know when his real birthday is, it doesn't matter when he celebrates it. Jinpei goes to the Jupiter mountains in order to research his real birthday and his origin.
Jinpei sleeps in the hut of an old man he met, but they are attacked by a Ninja group. Jinpei learns from the old man, that he used to be one of those ninjas as well and that, because he opposed Katse, his eyes were crushed while the chief and his family were killed. Only one person, the at-the-time three year old son of the chief, was missing. However, the old man says that if he were to meet that child, he wished he could convey him the message that knowing about one's origin is no luck. Then he breathes for the last time.
Soon, Jinpei meets with Ken and the others, who have stolen the chariots of the ninja group and, led by the horses, hurried to the base, and also with Jun, who sneaked into the base as well. They fight with the ninja group, who has been subdued by the Galactor army, and defeat the giant devil man, composed of the united ninjas, with the Tornado Fighter.
They couldn't learn Jinpei's origin or his true birthday. But as a reparation, Ryu hands Jinpei a birthday present. The present has been crushed in the fight, but Jinpei is nevertheless satisfied.
When the ISO intelligence office analyses a horn of a mecha which fell into the Mammoth Canyon, they conclude that with 80% probability the Galactor Headquarter is at the upper course of the Ielo river. Because the Ielo river is a gorge, the God Phoenix cannot fly into it, and Ryu is left with the God Phoenix at the entrance of the gorge. The other four head towards the upper course of the river in a canoe. However, on their way there somebody interferes with them. Elsewhere, this also becomes a hindrance to the Galactor operation of displaying the headquarter, thus luring the Science Ninja Team there. They capture the man.
Going up the river, they come across a sea deep below the earth, extending in the middle of a cave. However, it's the Galactor base. Just before the door in the ceiling closes, Jinpei escapes, but the other three are captured. Jinpei contacts the God Phoenix. Ryu is afraid somebody might listen in and pretends to be sleeping, not answering the call. Then he secretly takes off and steers the God Phoenix towards the base.
Caught in the base, the man hears what is said between the Science Ninja Team and Galactor. He seizes an opportunity and opens the ceiling. Jinpei immediately throws in a bomb and releases the bonds of Ken and the others. Taking the man with them, the four of them escape from the base. Ken orders to shoot a missile into the base. The Galactor base is blown up.
The man, having been rescued, tells them that in a fight between Galactor and the Science Ninja Team his willow at the bottom of the sea had been destroyed and he had taken it badly. However, he says that he made a mistake. Ken says that he knows that there are humans who are involved in his fight, and that the burden of his post weighs heavy on him.
From the UN rocket launch site the two-man rocket, Leona 3 is launched in order to solve the mysteries of the Milky Way Nebula.
Nambu leaves the launch site together with the president in a private plane, but then they are reported missing. The real president has been killed before the launch.
Suddenly, Leona 3 deviates from its course. The control mechanism in both the machine and the control center has no effect. As it stands, it seems that the rocket will crash on the Shaku peninsula, resulting in 20.000 dead and injured people. The Science Ninja Team is charged with the search for Nambu, who participated in the development of the control mechanism.
Nambu has been locked up in an atomic power plant on the Shaku peninsula. He gets in contact with a transmitter. Katse turns off the interfering radio waves on purpose, thus luring the Science Ninja Team there. Then he locks them up in the power plant together with Nambu. Telling them that Leona 3 will fall onto the plant, Katse escapes in a devil star disc plane.
They have a narrow escape from the power plant, however, since it is already too late to correct the course of Leona 3, Nambu orders them to shoot a rocket at Leona 3. The crew of Leona 3 is already prepared and has cut the connection as well. Ken is at a loss. However, when Joe wants to press the button, Ken does it.
Leona 3 disintegrates. Only the rosary, containing the last prayer of the crew, comes floating down towards Earth.
Joe, heading towards a meeting point, is blinded by a light reflection and runs into a woman. Seeing his mother's face in her, he takes care of her, but another blinding makes him feel afraid.
At that time, the God Phoenix is forced into a tough battle because the G-2 is missing. Joe, having returned, does not mention that something is not right with his body, and acts up towards Nambu. Nambu orders him to rescue the young air pollution specialist, Mekker, who seems to be developing the mechas. Nambu also asks Ken to secretly help Joe.
Joe boards a bird missile and the God Phoenix shoots it unnoticed into the mecha that has appeared. The mecha returns to the base. Joe sneaks into Mekker's room, accuses him of killing people with the poisonous gas he produced and knocks him down. Mekker wails that the world has ignored him, but that Galactor has appreciated and helped him. Joe provokes him, saying that he will let him take out the gun to shoot at him.
Just when Mekker shoots, Joe is attacked by another blinding. However, Ken breaks in and saves him. From the speakers, Katse's voice comes out together with poisonous gas and Mekker notices that he has been used. Ken and the others take Mekker with them and escape from the base. The mecha and the base are then blown up.
After returning, Joe visits the woman's room. He's afraid of that he may be taken off the Science Ninja Team because of his illness and that he won't be able to take his revenge.
The Science Ninja has pursued Katse and arrives at a base. X orders Katse to terminate the Science Ninja Team.
They want to reciprocate when missiles are shot at them from the base, but Joe can't focus properly and therefore can't decide on a target either. The bird missile he shoots blindly destroys the upper part of the fortress. The five of them break into the base, but they are guided into a trap and are about to be buried under sand. They escape with the tornado fighter, but because of Joe's blinding, they fail the first time. Ken notices Joe's condition and orders him to stay on the alert in the God Phoenix. Joe goes back to the God Phoenix and is irritated because he has the enemy before his eyes and can't do anything. He punches a panel and causes his fist to bleed.
Ken and the others discover an ammunition storage room and plan to use it to confuse the enemy, but through a trick of X they are locked up in a room with a drill attached to its bottom side. The room moves forward deep into the earth, heading towards the magma. Through the drill's centrifugal force there's nothing they can do. Ken contacts Joe in the God Phoenix, and tells him to shoot a bird missile equipped with a timing device right below the drill. When Joe says that he doesn't have self-confidence, Ken his convinced that something is not right with Joe's body. However, Ken tells him that he entrusts their lives to him and lets him know the location of the drill with a bird scramble. Joe prays that for one second everything will be well and back to normal. The eyes return to normal for a moment. Joe's fist punches hard on the launching button.
The Science Ninja Team escapes alive and well, but Ken, without reason, feels afraid at the sight of the blood on Joe's hand.
A by-product of the Mantel plan is the Mantel condensation energy formula whose immense destructive power is kept a secret. In order to bury that equation forever, Ken goes together with Dr. Maxim towards the North Pole Sea in a cargo plane.
Underway, a screw in the throttle comes loose and they get into trouble steering the plane. However, Ken puts in a clip as replacement and makes a forced landing. But the cargo plane is swallowed by a sudden crack appearing in the ice field.
When Ken and the doctor come round, a physician appears before them. He explains that twenty years have passed since and that the present is a world where Galactor has been victorious. Ken is not convinced and is shown the devasted surface of the Earth where the slanting ISO building and the graves of the Science Ninja Team are. Moreover, Jinpei, now grown up and a Galactor member, shows up. He says that they had been defeated, but that Ken should accept this peaceful world, and convinces him to hand over the equation data.
Dr. Maxim agrees to hand over the data. In order to take out the data inserted into his own body, he goes to a capsule in the cargo plane. Elsewhere, Ken goes to the cockpit and guesses that it's a Galactor trick since the clip did not get rusty. He sends a Bird Scramble. They corner Katse who is disguised as the physician, but Katse sets the self-destruct mechanism and manages to escape.
The party goes in the God Phoenix to the North Pole Sea again in order to submerge the data there. The Doctor did notice the trick very early and he had the intention of eliminating himself with the data in the capsule.
Ken is worried about Joe's condition and Joe is afraid of being taken out of the fight. A fight between the two is interrupted by a message from Nambu.
Secret ISO circuits are being tapped into and because of interfering electronical waves, the enemy cannot be determined. When Jun says that they may be able to determine the location if they use their bracelets, Joe wants to run off, but Ken stops him. Ken says that it's better to be a couple people only and proposes that he goes together with Jun. Joe gets the order to be on standby and hands Ken his airgun.
The two of them think that the helicopter on the roof the ISO headquarter is suspicious. They get in and accompany it to the base where they recover the tape from Katse. However, they understand that the tape has already been copied. The two shoot a wire into the fleeing Devilstar disc, but they land in the middle of a big swamp where there's no place to hide. The two are chased around by Galactor mobiles. Tied up, they are dragged along behind the mobiles. Joe has been following the transmitter placed into the airgun, and shoots the ropes holding them. Joe shoots down one mobile after the other. The mobiles unite and change into a mecha, which Joe confronts in his G-2. Evading the rays of light, he shoots the head with the Condor Machine and blows it up.
Joe's bold, smiling face has returned to Joe. However, his two opposing sides, self-confidence and puzzlement, are too much to bear.
A message comes in that a mecha has appeared, but since he can't contact Nambu, Ken goes out based on his own decision. But that mecha is bait to lure the team away from Nambu.
Meanwhile, Joe visits an unlicensed doctor. The Female Commander appears, unnoticed by Joe. The doctor watches Nambu, who has locked himself up in his house, pushing his analysing work. Nambu is abducted by Galactor. Joe, who has visited the doctor again, sees the commander, follows her and arrives at the mecha where Nambu is held.
Nambu says to the triumphant Katse that it's a pity that he can't publish the true face of Katse, which he has been grasping for a month. At that moment, Joe comes storming in in order to save Nambu. He is shot by the Megazainer, the transformation is undone and he remains unconscious. He is surrounded by Galactor rifle muzzles. At that instance, the Science Ninja Team, who entered because of Joe's message, mows down the Galactor members. Katse aims the Megazainer again at the Science Ninja Team. Regaining consciousness, Joe shoots the wire of his airgun into the muzzle of the Megazainer, making it explode. The mask goes flying through the explosion's shockwave and Katse covers his face. Nambu trusts them the secret that Katse should have been born as twins, one male, one female, but that he is a mutant who was born as a hermaphrodite.
Just then X shows his form before Nambu and the others. Ken hesitates for a moment to throw his boomerang at the fleeing Katse. The Science Ninja Team shudders at the existence and power of X.
The illness progresses and Joe goes racing at the track in order to shake off his fear. There he is captured by Galactor and dragged before Katse. Katse presses him to reveal the true faces of his comrades. Because he declines, Joe goes mowing down the Galactor members who assaulted him, but he is attacked by another blinding. On the way to the cell he escapes by jumping off the mecha, but he collapses on the street and is brought to a hospital. After regaining consciousness, Joe hears Nambu and the doctor talking on the phone and learns that he has still about a week or ten days left to live.
Galactor starts its last operation. Additionally, they start the Vibration operation as a bait.
Everywhere on Earth earthquakes of varying scale keep happening. Nambu gives orders to investigate the relation between the earthquakes and Galactor, but Joe is left behind for a medical examination. Joe asks Ken to take the G-2 car with him. When the Science Ninja Team leaves, Joe sees a moment of carelessness by Nambu and runs away.
Based on Katse's careless words, Joe finally reaches Cross Karakorum and is convinced that the headquarters are there. When he wants to contact Ken, his bracelet is smashed by a Galactor bullet. Joe fights with the Galactor members surrounding him. But finally he crumbles because of the Galactor bullets.
At that time, in an observatory, the extinction of the star Selector in the Andromeda nebula is observed.
The mecha serving as bait is destroyed by the God Phoenix. Then, the order from Nambu to search Joe comes in.
X is agitated because of the disappearance of Selector. He accidentally tells he will have the Earth extinguished and orders Katse to set the timer in the mantle.
The order to return home goes out to the Science Ninja Team. It is said that the Earth is turning into a black hole, that neutron reactions have been happening. Nambu says that Galactor is causing nuclear explosions in the interior of the mantle layer. But they can't determine the location. At that moment, the message that the headquarter has been discovered is received by Ken's bracelet in morse code. Nambu suspects a trap, but sends the Science Ninja Team to follow the signal in the knowledge that it might be a trap. Those who are sending the signal are the two members of Red Impulse who sneaked into the headquarter.
Joe is given a drug which lets him recover temporarily and is dragged before Katse. Hearing about the Black Hole Operation, Joe throws a feather shuriken in Katse's direction. But Katse evades it. It is then drawn into the interior of the machine by the counter. In the eye of the collapsed Joe, the God Phoenix on the screen is reflected.
The God Phoenix has arrived, but the fog is dense and they don't know the entrance. Then the Red Impulse members appear and lead the Science Ninja Team. But they fall into a Galactor trap and the two men collapse under the bullets. The Science Ninja Team, with the volition of Red Impulse in their hearts, return to the outside. They split up in different directions, searching for the entrance.
Eerie stone statues appear in the fog. The Science Ninja Team walks around, searching for the entrance. Galactor is there and has spread out a radio net, waiting for a transmission to be sent. And also Joe, who has learned of the arrival of the Science Ninja Team, has mobilized his last forces and has sneaked out of the base, where people were trying to get away.
In the middle of the fog, Jun is cornered by Galactor, but Joe's feather shuriken saves her. Through the radio communication, saying that Joe has been discovered, the four other team members gather around Joe, but Joe's hour of death is already impending. Leaving some parting words, Joe tells them that the entrance to the base is here. Intercepting the radio communication, Galactor comes to shorten the harmony of the gathering.
Ken and the others head towards the entrance, leaving Joe behind. Breaking in, they discover Katse and push him to stop the operation. However, X's figure appears and he tells them that in 30 minutes Earth will have disappeared. Katse presses him that he had said something else in their conversation. X tells him that the disappearance of his mother star has caused the plan to change, then he shows his figure, a huge golden tube, and leaves. The team wants to stop the mechanism, but Katse says that he has trusted X and has put in no control mechanism, then he throws himself into the magma.
Ken wants to climb into the mechanism and stop it, but Jun holds him off. At that moment, the feather shuriken Joe threw at Katse loosens a gear wheel inside the machine. Because of a molecular bomb which exploded in the interior of the machine, the mechanism stands still. However, nobody knows that.
Ken and the others go outside, and stand still on the solid earth with no survivors around.
Nambu reports on the self destruction of Galactor at the press conference. He answers to the reporters that the core of evil is in his own heart as well as in the others' heart as well.