The Science Ninja Team follows Nambu's orders to come to Huntwall to spend their free time there. Only Ken doesn't trust those instructions. At that moment, a man in a white suit, being pursued by the police, appears and Ken helps him. But when they hear from the police commander that that man is a Galactor, the Science Ninja Team is on alert. While flying his Cessna, Ken is attacked, but saved by the Red Impulse commander. The man in the white suit is the Red Impulse commander. He asks Ken for help to get the legal proof that the defense minister of that country concluded an agreement with Galactor. He then tells Ken that he spent 10 years to stop Galactor's plan, abandoning his family. The two sneak into the mansion of the defense minister and get their hands on the film proving the agreement. However, they are discovered. The Red Impulse commander tells Ken to give the film to the president, then they split up. On the following day, when they come to the presidential manor to hand over the film, the Galactor mecha Kataroller shows up right in the middle of the president's birthday party. It picks up the mansion and lifts it into the air. But through the Science Ninja Team, the people could already escape and the mecha, having failed to assasinate the president, goes away. Ken hears from Nambu that he can meet his father once this task is finished and goes off, his heart full of longing thoughts.

To be able to see his father! Carrying this wish in his heart, Ken follows the whereabouts of the mecha. Before him somebody is shot and wounded. It's Sabu, a friend from Ken's childhood. When Sabu sais that he saw Ken's father in Huntwall, they both go there. In Nambu's office, Katse makes a bold appearance in disguise. He leaves saying that if the world does not surrender to Galactor in Huntwall, the V2 plan will be realized. The V2 plan is the terrible plot to make the Van Allen belt descend with a special rocket, thus extinguishing mankind with radioactive flames... Nambu orders the remaining four team members to stop the rocket without Ken. But the teamwork breaks apart and they can't use their missiles. The God Phoenix is surprised by the mecha and with skill they manage to defeat it, but they were definitely at a disadvantage. Meanwhile, Ken has met Sabu's treason and is held isolated by the defense minister in order to lure the spy Kentaro Washio into a trap. But coming to the rescue is Red Impulse. He scolds Ken that now is not the right time to ask such sweet things like how his father is. He then tells him the actual situation. Joe and the others have arrived in Hontwall, and before their eyes, the rocket takes off into the sky. Blaming the fact that Ken was not there, the Science Ninja Team is told by Nambu that Red Impulse himself is Ken's father.

The Galactor rocket explodes in the Van Allen belt and humankind enters the worst crisis ever. Upon the message from Galactor saying that a rocket restoring the belt will be launched if the world surrenders within 24 hours, the representatives of all countries assemble. They feel the time pressure and want to come to a conclusion. Nambu tells them to believe in the Science Ninja Team and puts an autolock on the doors so that they won't open until the following morning. The Science Ninja Team is mobilized to take away the Galactor rocket and to restore the Van Allen belt. At approximately that time, Ken sneaks alone into the construction facility for the rocket. In order to complete the rocket within the timeframe, it is changed from automatically controlled to manned. Ken, in the middle of Galactor members who are sleeping, tired from the now finished incessant work, emits a bird signal. But then Katse's gun is pointed at him. Ken transforms into birdstyle. The gun of the Red Impulse commander, who sneaked in as well, is then pointed at Katse. The God Phoenix breaks in and Katse escapes and the defense minister falls to his death. Taking the responsibility, Ken says he will get into the rocket himself. Jun then tells him that Red Impulse himself is Ken's father. The dream of Ken to reunite with his father also becomes their eternal separation at the same time. The Red Impulse commander throws Ken away and gets into the rocket himself. Ken runs after him, calling for his father. In Red Impulse's mind, the figure of Ken in his youth is turning around. The rocket disperses across the sky and Earth is saved.

Katse, who got into his stride by the funeral of Red Impulse, plans to destroy institutions related to uranium in the whole world. The representatives from all the countries assemble at the ISO, and a conference to discuss countermeasures is opened. The Science Ninja Team acts as guard. Ken alone separates himself from his friends, lost in mourning over the death of his father. At that time, he discovers a dead body in the middle of a fountain. Because the flag of the country of Atarii is attached to the body, Ken penetrates into the conference room and captures the Galactor who poses as the representative of the Atarii country. After returning to Crescent Coral, Ken makes the man spit out the location of the headquarters by continuously torturing him. Nambu slaps Ken, saying that his behaviour is not excusable by the fact that the man is a Galactor. Ken turn his back towards Nambu and forces the other members of the Science Ninja Team to go with him. Guided by the man, they go to the location. But in the base, which is only a common one, they encounter an ambush by Katse. They end up getting trapped in a room with walls made from ice from the north pole. Katse raises the room's temperature, thus causing the ice to slowly melt. He then leaves to attack the uranium institutions. Joe and the others blame Ken, that his behavior, which is solely aimed at revenge, caused all this. Ken wails whether they know how it feels to have a father killed. Jun rebukes him that he is not the only one without parents. Those words cause Ken to get back his calmness. The Science Ninja Team escape from the ice chamber and blow up the base. They pursue the Mecha in the God Phoenix and demolish it with their missiles.

The sea takes up 70% of Earth. Galactor makes Nambu and the Science Ninja Team chose between their lives and pollution of the seas by PCB. Pretending to agree, the God Phoenix goes to the pre-defined area in the sea, but when they blow up the approaching mini submarines, the pollution matter streams out and the Tarushia Sea ends up polluted. Ken discovers three tankers which seem to control the mini submarines and, using the mini submarine loaded into the God Phoenix, sneaks in. There, cleaning work is done for the returning mini submarines. Ken is discovered by Galactor. He defeats them and heads towards Katse's whereabouts, but in the meantime the tankers have transformed into one huge tanker which emits a magnetic force attracting the God Phoenix whose hull starts to crack. Ken pulls the control lever. Katse, activitating the self destruct mechanism of the tanker, escapes into a passageway beneath the floor. Ken pursues him, but Katse escapes in a rocket. Ken and the Galactor members go out into the sea, but the pollution matter flowing out of the tankers is approaching them. The Galactor members each die as they touch the pollution matter. By a hair's breadth, Ken is picked up by a mecanical arm outstretched from the God Phoenix and thus escapes the danger. Soon, the Galactor cleaning capules are released into the sea and it gets back its former beauty.

Jun is attacked by a group of bikers. Koji saves her, he is a former race champion and Jun's friend from childhood. Now he has become the commander of a Black Bird squad and is on the way to blow up the missile base of a certain country. When he wants to install the time bomb, the figure of Jun, the way he encountered her, crosses his mind. Without installing the time bomb, he runs away from the base. Jun sees his figure and reports to Nambu. She disagrees vehemently however when her comrades voice the opinion that Koji is a Galactor. Koji, who didn't fulfill his task, is ordered by Katse to assasinate the President during a bike race which the President will be watching. Jun goes to that race, in which Koji participates, only very reluctantly. But she agrees when Ken says that they will try to save him if possible. Koji's attempt to assasinate the President is foiled by Joe's sharpshooting and ends up in failure. Koji seeks refuge in the officers' mansion. Jun follows him and sees how Koji gets orders from Katse. Koji notices Jun as well. The bikes of the Black Bird squad transform and unite into a snake-shaped mecha which starts to attack the God Phoenix. In order to defeat the mecha, Jun presses the launch button for the missiles. When Koji is defeated by the Science Ninja Team, he decides that this is the punishment for his own crimes.

Mike Miller, a sniper, has been released from prison after 35 years. Galactor gives him a small tank with a freeze gun on board and orders him to eliminate the Science Ninja Team. Three observation satellites high above the south pole are shot down. Guessing that this is Galactor's fault, the Science Ninja Team heads towards the South Pole. Katse is awaiting their arrival, accompanied by a small tank. Joe tells Ken to pursue Katse and goes after the tank, but the freeze gun freezes him along with the G2 car. The rest of the team heads out in order to fight in their individual machine, but when Ryu sees how Jinpei is done for, he heads towards the tank without thinking and the G-5 gets frozen as well. But when Mike aims at Jun, he hesitates one moment and the bullet misses. Besides, the gun is starting to burn because of the continuous use. The fire is fanned by the G1 and the fallen over tank goes up in flames. Ken and Jun approach Mike. He asks them why they didn't fight using weapons. Ken answers him that their individual machines are not equipped with weapons. Mike shows Ken the cores of the bullets he secretly took away and tells him that his comrades are not dead. He also says that he missed the shot at Jun because he saw in her figure his daughter from whom he was separated 35 years ago. Then he dies. Inside the God Phoenix, which is on its way home, Ken says that if they wished for weapons, it wouldn't be them to try outdoing Galactor.

The Jet Cutter, developed by the ISO to gain energy without causing pollution, is stolen. Nambu gives the order to recover it. Ken opposes him, asking whether they have to pay for the faults of the ISO. It's because of a lack of reason which makes him think that he wants to attack the enemies of his father. Jinpei starts crying at the argument between the two men. When Ken sees this, he reluctantly agrees to be mobilized. Ken and Joe enter the cave where Mekabutta disappeared and are attacked by buddha statues acting as surveillance devices. Ken ignores Joe who suggest they should return to the God Phoenix for the time being, and he runs towards the interior. Joe follows him, but is hindered by the fire being spouted by the buddha statues. Ken discovers the Galactor base and Mekabutta in the interior of the cave, but gets knocked unconscious when he touches an iron grating with high voltage which comes falling down. When Ken wakes up in the God Phoenix, Mekabutta has already left the base and is heading towards an uranium mining factory. The God Phoenix pursues Mekabutta, but the Jet Cutter is loaded aboard the mecha and it spouts continuously heat of 40'000 degrees celsius from its four faces, on each side one. The God Phoenix has to fight hard against it. But Ken, using the multiple firebird figure, lets the Jet Cutter shoot without pause, thus causing Mekabutta to self-destruct because of overheating. In the God Phoenix, on the way home, Ken apologizes for being hotheaded because of this desire to fight the enemies of his father. Joe tells him that if they defeat Galactor one by one, Katse will be cornered.

A fishing-boat is in the vicinity of Ghost Island and becomes eyewitness to a big ray and cuttle-fish. Afterwards, it is swallowed by a huge waterspout and is shipwrecked. On Nambu's orders, Ken and Jun land on the island and start to investigate. As night falls, the two of them see how previously defeated Galactor mechas appear explode as they are swallowed by a waterspout. They are convinced that there has to be a mecha factory. They defeat Galactor members who have come searching for intruders and take their place. Then they sneak into the base. In the base, Doctor Ogawara and his assistant Nakamora are about to explain the new mecha Komaking to Katse. Ken tells Jun to contact the God Phoenix, then he gets into the mecha. But Jun follows him, sneaking in as well. The God Phoenix fights hard against the waterspout created by Komaking. But Ken and Jun destroy the power generator of the mecha and it starts to fall. Ken catches Katse in the command room and brings him back to the God Phoenix. Fulfilling a wish he has since a long time, Ken pulls off Katse's mask. But the face appearing beneath it is the one of Nakamora. Katse has already escaped. When Ken weeps tears of anger the words of his father seem to resound in his ear, encouraging him.

During an experiment with Galactor's brand-new mecha, the research machine crashes. Katse commands the termination of the survivors. The Science Ninja Team arrives at the crash site of the machine. It is not clear what the purpose of that machine was. They discover a young man and bring him back. The young man has lost his memory. He and Jinpei become good friends. When the name of Galactor is said, the young man shows a strong reaction in his motion nerves. He goes out on a motorcycle together with Ken. They are attacked by Galactor and from that shock, the young man remembers the location of the base, the weak points of the mecha and also that he himself is a Galactor. Ken wants to go to confront the mecha and take the young man with them. The young man declines, suffering from the fact that he's Galactor. However, Ken convinces him to go with them. Jinpei then addresses him as "Science Ninja Team G-6". Ken and the young man sneak into the mecha. While Ken attracts the enemy, the young man seeks the device to reverse the flame and laser gun, the weak point of the mecha. However, he is captured by the commander and told to shoot Ken with the gun given to him. Ken tells him to think this over. The young man points the gun at him, saying that this is his destiny. The bullet and Ken's boomerang fly away at the same time. The bullet pierces the commander, the young man is hit by the boomerang. He tells Ken where to find the reverse mechanism, then he breathes for the last time. In his report to Nambu, Ken tells the following: Through G-6's death defying deed, the mecha could be blown up.

Ken is flying over the country Hontwall in his G1 plane. He is shocked when he sees the three Red Impulse planes. The figure in one of the machines is undoubtedly his father. When the Red Impulse commander asks him whether he should lead Ken to the new base, Ken gets into contact with Nambu. However, without listening to Nambu trying to stop him, Ken heads towards the base. Nambu orders the God Phoenix to investigate what is going on in reality. However, the God Phoenix encounters a mecha without the G1 on board. It is caught and brought to the base. Ken asks Red Impulse why he didn't let him know that he was alive. Red Impulse answers that it was because he was looking for the Galactor Headquarter. He says that he would like Ken to hand a briefcase to Nambu containing information regarding the location of some bases. When Ken brings the briefcase to Nambu, he learns that they didn't get any report from the God Phoenix. In order to make sure of the real intentions of Red Impulse, Ken goes back to the base. Because Red Impulse uses some delicate words, Ken understands that Red Impulse is an imposter. The commander is Katse in disguise and there was a transmitter installed in the briefcase. Ken gets angry and grabs Katse by the collar. However, Katse takes advantage of an opening and gets away. Ken is dropped into a subterranean prison under the floor. His abducted team mates are there. Ken escapes from the subterranean prison and contacts Nambu, telling him to get rid of the briefcase. The signal of the transmitter is interrupted and the mecha follows the small transmitter Ken attached to Katse. The Galactor base and the mecha end up attacking each other and are destroyed.

A celebration is held in order to praise the merits of the Science Ninja Team. However, the participants are super robots. They were invented by Nambu with purpose. His plan is to let them be intentionally captured by Galactor. Then based on their message, learn where the location of the enemy base is, have the real Science Ninja Team sneak in there. But Ken thinks that the enemy will not be fooled by them, so he takes the place of his robot. As Nambu intended, a Galactor mecha appears, freezes the robots and Ken with a freeze ray, and takes them to the base. After being thawed, Ken mingles with the robots and sends a bird scramble. The God Phoenix receives the signal and hurries towards the base. But the robots explode upon touching high voltage electrical current. It becomes obvious that they are fakes. The mecha is deployed. Ken sneaks in the mecha and throws robots' debris into the propulsion system. The mecha crashes and goes up in flames. Ken is dead. With their breath held, his comrades look at the screen in the God Phoenix for a long time. Before them, Ken's figure appears slowly falling, having escaped by using the robot's capes as a parachute.

Professional baseball players disappear in front of the spectators during a short power outage in the middle of a match. Nambu thinks that it's Galactor's fault and according to his instructions, the Science Ninja Team are keeping guard everywhere in the baseball stadium. During another game, a similar power outage happens, and the players disappear before their eyes again. This time however, Jinpei, who was acting as a ball boy on the field, has disappeared as well. The remaining four team members go to investigate the ground thoroughly in the middle of the night. But suddenly the surface of the earth breaks open and Ken and Jun fall into a secret subterranean base. They are made to inhale some gas and are taken into a cell. Jinpei is already in the cell. He says that the players are brainwashed by some kind of drug and are to receive a special training in order to turn them into Galactor members. The three of them escape from the cell. Katse tells them that during the match this evening under the floodlight, a hydrogen bomb might explode. It would be capable of blowing away the whole country. Then he escapes. Ken contacts Nambu. Joe and Ryu start to search immediately for the bomb on the surface, but the game has already begun. Ken gets information from the commander that if a homerun ball hits the backscreen, the fuse will be activated. A homerunball is hit. Joe and the others aim at the ball flying towards the backscreen. All four weapons miss their aim. However, the ball is knocked away just before hitting the backscreen. The ball falls to the ground and it is pierced by Ken's boomerang.

A year earlier, the northern country Flanbel escaped from the rule of the Dictator General Somure. But Galactor, who instructs Somure, appears in the mansion of the Prime Minister and tells him that he either obeys or dies. By the demand of the governor, the Science Ninja Team sneaks in through the secret back door. On the peace memorial day, presents are distributed to the children by the governor. But the Suimusa group, which Jinpei met, have their presents stolen by children from the upper city quarter. That night during a patrol, the Science Ninja Team discovers that all the families which opened the presents are dead. They learn that the governor is a subordinate of Somure and has put poison gas into the presents. Meanwhile, the Suimusa group has gone to the celebration site in order to tear down the snow man to vent their anger. However, that snowman is the camouflage for Galactor's mecha. Mistaking the shapes of the Suimusa group for the Science Ninja Team, Galactor captures them. But they are saved by the Science Ninja Team who follow them and take them aboard the God Phoenix and escape. The mecha pursues them. In the interior are the governor and Somure. Burying the mecha together with Somure and the governor, the God Phoenix leaves. Inside, the Science Ninja Team says they want to make a present as replacement for the ones the Suimusa group missed. The Suimusa group replies that the best present was to have been able to fight alongside Gatchaman. The voices of the children echo "Justice will win for sure!"

The conserved brains of famous doctors keep getting stolen. A monster also steals the brain of Dr. Yamashina, an expert in robot engineering. The Science Ninja Team follows it, but lets it get away. But Nambu gets a hold of one of the tentacles from the monster. Analysis shows that the monster is the low life form Bem from space. Nambu fears that if Galactor's scientific powers can control space life forms, they may be able to revive the dead brains. At a scientific exhibition, Dr. Yamashina's creation, the X1 robot X1, is planned to be revealed. In order to achieve that, Director Anderson requests protection for it. At the exhibition, Bem appears, unites with X1 and escapes. The God Phoenix pursues it, and discovers Bem again at the spot where it lost sight of him before. Galactor has Bem and the robot unite. With the brain energy of the doctors Superbem is completed. Ken has it followed by the God Phoenix and sneaks into the base himself. In the base, the commander guiding Bem notices that a brain don't have enough output. In reality, the stolen brain of Dr. Yamasina is an imitation placed by Nambu on purpose. Ken sneaks in there and destroys the energy source for Bem. His plan having failed, Katse orders the self-destruction of Bem. Bem and the base explode together and the God Phoenix, uniting with the G1, escapes the explosion using the Firebird.

The queen of Monarins is a fan of the Science Ninja Team. Every year, she donates large sums of money to the ISO. Katse comes into the country himself, planning to weaken the activities of the team by killing that woman. They get word that Galactor may attack during the fashion show and the Science Ninja Team is put on guard duty. In the middle of the night, while Ken and Joe are investigating the surroundings of the palace, they get attacked by some ominous figures. Jun gets hired as a model for the fashion show. Shortly thereafter however, Katse and the Devil Stars take the place of all the participants except for Jun. Jun enters the palace and notifies the queen that the team will be at her side. In the final stages of the show, the designer announces an original design that turns out to be the Devil Stars. The queen calls the name of the Science Ninja Team as the fashion of justice. As a result of the special training, the team evades the Devil Stars. Katse escapes alone.

Katse, opposed to Sosai X's orders to destroy the Mantle Plan, asks whether it wouldn't be better to conquer Earth after the Mantle Plan was finished. X promises to Katse the rank of President Z and lets him start the operation. But behind his back, X laughs and says that Z is a symbol for murder. Institutions of the Mantle Plan are attacked one after the other by a jellyfish mecha. The God Phoenix faces it, but its missiles have no effect. On the contrary, the launching ramp gets hit. The God Phoenix wants to escape with the multiple firebird. But mines are released upon the God Phoenix and it is wrapped in flames in no time at all. The God Phoenix makes a forced landing in the desert and explodes in the end. While the rebirth of the God Phoenix is being carried out by the ISO, the Science Ninja Team has no means to intervene and can only watch Galactor's attacks. They are in an irritated state when they receive the message that the revived God Phoenix is finished. Each of their individual mechas has been outfitted with a weapon. But Nambu tells the five team members that the purpose of those weapons is not to kill, but for defending themselves. When the message arrives that the jellyfish mecha is attacking the ISO headquarters, the God Phoenix is deployed immediately. Guiding the mecha to a mountain region, they defeat it with the weapons on their invidivual mechas and the Super Bird Missiles. But in Ken's heart there is the doubt that if the development of new weapons continues, peace might still be far away.

One day on a small island in the south sea, a nuclear explosion takes place. The ISO research planes crash and burn in the high radio-activity. From the remaining records, they learn that in the vicinity of the island there's radioactivity, but not in the center of the island. The God Phoenix is supposed to go to investigate, but in order to overcome the radioactivity belt, they have to use the Firebird on the way in and out. Beauce of this, they request a research ship to supply them with fuel. When they enter the island, there's no radioactivity, and the buildings are also undammaged. But there's nobody around. Joe sees human shapes in a tram which were exposed to very high heat and instantly made molten. He is convinced that a nuclear experiment has taken place. At that time, the walls of the buildings suddenly start to come loose and the radioactivity gets very strong. They get into the God Phoenix and escape from the island, but because of the shock caused by the radioactivity belt not being there anymore, they all lose consciousness. When they wake again, they are on board the research ship. There, Nambu is waiting and says that because of a change in plans they will return to the base in the God Phoenix. Ken is about to obey, but when Ryu says that, for passing the radioactivity belt, they didn't use any fuel, he turns towards Nambu and throws his boomerang. Nambu is Katse in disguise. The strategy of Galactor - namely to pose as Nambu and to be led to the base in the God Phoenix, has failed. Katse escapes in a disc-shaped plane.

Galactor sneaks into the country Shosken, 80% of which is taken up by the Ohara desert and mountainous regions. Communications break off with a special troup which went there to investigate in the old tombs. In order to search for them, the Science Ninja Team splits up and mixes with the citizens. A woman confuses Jinpei with her dead son. But he sees his mother in her as well and goes to her house. There he hears the story that in the old tombs, which are called the devil's cemetery, caravans and people from the village disappear. Jinpei thinks that those tombs are suspicious, and sneaks in there alone. He finds a Galactor base where they are trying to gain uranium from underground quicksand. The people who disappeared are made to work there. Jinpei calls Ken and the others, who join him. Together they corner Katse. But Galactor has taken the village people as hostages and they are forced to release Katse. Nevertheless, Galactor wants to drop the hostages into the quicksand. But Ken's boomerang flies towards them. Galactor members are about to fall unto the self-destruct mechanism of the base. The self-destruct mechanism ends up being activated. Katse and the Galactor members escape. Ken and the others guide the village people hostages outside of the base. The woman is worried about Jinpei and wants to return to the tomb. But is stopped and collapses crying. Jinpei appears as a member of the Science Ninja Team and cannot show his face to the woman. After returning to the God Phoenix, he has a good cry clinging to Jun's chest.

Mummified corpses keep being found. Since the dammages continue, Nambu orders the Science Ninja Team to find out the cause of all this. During a patrol, Joe saves a girl from a taxi which is being attacked by mannequin mechas. He takes her to the hospital. But Ken blames him for not contacting him from there and doesn't trust the girl. Joe returns to the hospital and sees the girl running away from her hospital room. He also sees the nurse who has been assaulted. Joe follows the girl. The girl notices, and her face shows a slight smile. Ken, who has received a message and come to the hospital, brings back a piece of plastic from the bed the girl was in. There he receives a message from Joe, saying "the cemetery of the puppets" and then breaking off. Connecting the plastic piece to Joe's message, the Science Ninja Team searches for a mannequin dumping place. However, Jun and Ryu are also captured by Maya, the girl who controls the mannequins. Through Ryu's Birdscramble, Ken and Jinpei sneak into the base and save the other three. Then they defeat the mannequins. Maya was allowed to leave Galactor if she succeeded in terminating the Science Ninja Team. But Katse shoots Maya, who failed, and goes away saying that it is not possible to leave Galactor alive. The masks falls from Maya's face. She tells the Science Ninja Team about the self-destruction of the base and murmurs that she would have loved living under the sun, then she passes away.

The ISO discovers a new energy source in the Himalaya, but an investigation troop sent there is annihilated by the Yeti. Because of several rumours about Yetis, Jinpei goes to the Himalaya alone. There he is attacked by the Yeti, but it is a Galactor Yeti Mecha. The God Phoenix goes to the Himalaya to look for the missing troop according to Nambu's orders. They get the message from Jinpei about the apparition of the Yeti and head towards the location this message came from. Elsewhere, matters have developped in such a way that Jinpei has been saved by Galactor members and is now working as a servant in the base. While working, he secretly sends a bird scramble signal. Additionally, when he brings food to Katse's chamber, he hears there Katse speaking with X. The God Phoenix appears in the vicinity of the base and Galactor turns towards it, attacking it with missiles and flame throwers. However, because of Ken's tactic the God Phoenix keeps turning back and while it is continously shot at, an avalanche gets started and the base is hit hard. The God Phoenix breaks into the base. Ken and the others corner Katse again. Ken tears away Katse's mask. Katse covers his face and from behind him, X appears with a flash and introduces himself as the ruler of Galactor. The Science Ninja Team is blinded by the light and they lose consciousness. When they wake up again, Katse and X's form have disappeared. A certain anxiousness arises now that they are aware of X's existence. The mountains of the Himalaya still enclose that secret.

In Amazonia the old entemologist (insect researcher) Toda who is continuing his research, notices unusal behaviour in the locusts. He notifies every authority and department, but he is not taken seriously. Jinpei, who heard his story, returns with him to Amazonia. The unusual appearance of the locusts is a Galactor deed. With a guiding radio signal emitted by a locust mecha a swarm of locusts is made to attack the city. In the research hut of Toda, they are attacked by a swarm of locusts. While protecting the hut with a pesticide, they capture the mecha locust leading the swarm and Toda finds out the frequency of the radio signal. However, because of the interfering radio signals, Jinpei cannot contact Ken and the others. He comes up with a plan and sprays the form of the bird head shape into a meadow with the pesticide. Having received a message about the unusal appearance of the locusts, the God Phoenix has come to Amazonia. They discover the mark and join Jinpei and Toda. Because of the appearance of the God Phoenix, Katse accelerates his plan and releases mecha locusts and their locusts swarms, heading for the capitals of the world. Ken hears the story about the radio signal from Jinpei and has the God Phoenix emit the the same frequency. He lures the locust swarms released in the world towards the sea and blows them up with a rocket. Only Ken and the other know that the true credit belongs to the old scientist who piled up years of research and was ignored by everybody.

The Science Ninja Team vanquishes another mecha and has let Katse escape yet again. With Nambu's transmission, they follow the course of Katse's rocket. However, Katse has switched to a car and heads towards a jungle. The Science Ninja Team descends towards the jungle as well in his pursuit and separates into three parties, searching for Katse. X receives an SOS signal from Katse and, together with sending a commando unit, takes additional steps by setting traps in the jungle. Joe criticizes Ryu for approaching a trap unprepared. But when he distrusts a wounded young deer, Ryu retorts that there's nobody more insensitive than Joe. Meanwhile, Jinpei discovers Katse and corners him, but is in turn caught by the commando unit. Before an ice covered mammoth, Joe and Ryu discover Jinpei about to be turned into a human sacrifice. They save him and additionally corner Katse, who changed into a shinto-priest. But Katse seeks refuge in the mammoth mecha and attacks Joe and the others. They are saved by a hair's breadth by the God Phoenix and Joe wants to shoot a rocket into the mecha. But when he sees a group of deer below the mecha, he hesitates. Luring the mecha into the mountains, they shoot at the ground below the mecha with a rocket. The mecha disappears into an avalanche. The Science Ninja Team is wrong in assuming that, because of the jungle with the traps set, the headquarter is nearby. Its existence is however still shrouded in the fog.

The mammoth which should be buried in a glacier, appears at an amusement park where Jun and Jinpei have gone. While saving the children, Jun's shoe falls off and gets stuck between the mecha's claws. Jun reports the loss of her shoe. Nambu tells her to look for it. He says that, with Galactor's scientific power, they might be able to discover the secret of the transformation from the shoe. In the Galactor base, Katse orders the analysis of the shoe which remained completely intact after burning in the incinerator. At last they find out the frequency of the electrical waves which cause the shoe to transform into a white boot. X has Dr. Mizuno start developing a weapon to undo the transformation. Additionally, they start searching for G-3 based on the data gained from the shoe.16 year old girls are recruited for a beauty center. Jun, who is depressed because of losing her shoe, applies for the job, even though she knows that it's a trap. The female commander, who has captured the four other candidates besides Jun, puts them to sleep and transports them to the base. Jun pretends to be sleeping and transmits a bird scramble signal. Jun is led off to the base and questioned by Katse. When it's almost too late, the God Phoenix appears. Jun seizes the opportunity and saves the girls, recovers her shoe and gets into the God Phoenix. Katse fires the rockets of the mecha, but because of the guiding system built in by Ken, the rockets return and the base explodes together with the mecha.

While a Galactor mech is mobilized, one of the small planes loses speed and collides with the fisher boat on which Ryu's father is. The boat is shipwrecked. When Ryu's younger brother Seiji hurries to Ryu's whereabouts and tells him of his father's shipwreck, Nambu's mobilization order goes out. Ryu desperately shakes his brother off, who is crying and clinging to him. But he ends up being late for the mobilization and the main research institute is already destroyed. Shortly thereafter, while they are doing bodyguard duty for a tanker, Ryu is worrying about his father's shipwreck as well and misses the course. In the meantime, the tanker has been attacked. Nambu scolds him that he didn't do his best. Ken defends Ryu and tells Nambu that they are not robots which just follow orders. Nambu tells them that they are under house arrest. However, Ken and Jun hear from Seiji about the shipwreck of Ryu's father and go out in the God Phoenix searching for the father without Nambu's orders. On one of the Amana islands they discover smoke and save Ryu's father and his comrades who are safe and sound. At that time, Ryu's father, without knowing that Ryu is his son, tells them the weakness of the mecha. Namely - when the small planes detach themselves from the main part of the mecha, the interior becomes visible. Aiming at an uranium store, the mecha appears again. The God Phoenix is mobilized. As he learned from his father, Ryu makes a rocket hit right on target into the main part of the mecha right after the small planes have detached themselves. The mecha is defeated.