A huge turtle-shapes mecha, the "Turtleking" attacks a uranium storage facility. The ISO and the delegates of various countries are very concerned. Nambu, the only person who previously knew of Galactor, now officially anounces the existence of both the criminal organization "Galactor", as well as the Science Ninja Team that has been formed to resist them. The Science Ninja Team receives Nambu's orders, unites in the God Phoenix, and flies off right away to a missile launching base where the mecha was sighted. Ken stops Joe, who's eager to get into his first real fight. Ken takes Jun along and they sneak inside the mecha. With Ken's help the God Phoenix then enters the mecha and Joe, Jinpei and Ryu join the battle against the Galactor members. Elsewhere, the commander of the mecha tells Berg Katse of the Science Ninja Team's existence. Katse then relays the message to Governor X. In accordance with X's instructions, Katse orders the Science Ninja Team to be destroyed. The order is to have the mecha make a suicidal plunge, taking the God Phoenix with it, thus burying the Science Ninja Team. But at the very last moment, the God Phoenix escapes the mecha by using the Firebird Effect.

A spaceship disappears, along with a device that can report and record the location of the Earth's resources. The Science Ninja Team receives Nambu's instructions and heads towards the bottom of the sea, in the vicinity of the spot where contact with the spaceship was lost. There, prawn-shaped bulldozers leave a huge aircraft carrier located on the sea bottom to build a uranium factory. Ken stops Ryu who wants to fire a Bird Missile, and sneaks into the aircraft carrier alone.

Deadly crashes involving passenger planes keep happening. Ken, who's investigating these occurrences, encounters a boy named Makoto. The boy is awaiting the return of his father who was reported missing in one of the accidents. Makoto's father is the younger brother of the inventor of Uranless, Dr. Takahara. The string of plane crashes has been caused by Galactor. They are intent on getting the Uranless, since it is capable of neutralizing the means of propulsion of their giant mummy. Ken has encountered the mummy in his Cessna before, and because of that incident, he has data concerning the propulsion system of the mummy. He contacts Dr. Takahara in order to get the Uranless.

During the investigation of an incident, Ken visits the Institute for Earthquake Research. Because of an earthquake caused by a mecha, he falls along with the director of the institute, into a crevice in the earth. Ken transmutes and is saved, but he cannot rescue the director. Ken stands before the director's grave and is attacked by the director's daughter Naomi, who firmly believes he's Galactor. Ken understands her anger at not being able to avenge her father and decides to let her know about his true identity as member of the Science Ninja Team. Consequently, he lets her join the team on the mission.

Oceangoing ships from the ISO keep disappearing. It always happens in the vicinity of a place called "Cemetery of the Sea". Director Anderson and Nambu ask the Science Ninja Team to go to a base on the ocean floor which is most likely to be struck next. The Science Ninja Team gets Nambu's message and takes the God Phoenix towards the base at the bottom of the sea. Then they encounter a mysterious submarine, which leads them to the Cemetery of the Sea, where they see countless sunken ships.

Gold bars are stolen from the vault of the World Bank. It is the deed of Galactor's Mini Robots. The Science Ninja Team get their instructions and start a search on the islands in the vicinity of the place where the gold bars seem to have been taken. Joe makes sure that Ken, Jun and Jinpei, in civilian wear, attract the enemy's attention and get taken off to the base. He proposes that if this is the headquarters, it should be destroyed right away. However, Nambu stops him by saying it's not the Science Ninja Team's duty to attack. Joe leaves a bored Ryu behind in the God Phoenix on the bottom of the sea and sneaks into the base in order to prepare for retaking of the gold bars.

There's a new kind of plane that does not pollute the environment. In the middle of Ken's test flight of this ISO-developed plane, he is attacked by a biplane, piloted by a man who introduces himself as "Katzen Berig". Katzen Berig lashes with his whip at the ISO plane, causing it to crash, but Ken saves himself just in time by deploying a parachute. Nambu suspects from the name that Galactor is involved and orders the God Phoenix to attack immediately, but the God Phoenix's tailfin gets damaged by the whip. Analysis of the material stuck in the hull of the God Phoenix reveals that this kind of metal, called "super metal whisker", is something that has been researched by the ISO, but not manufactured. Nambu is taken aback at the scientific power of Galactor, but when the production factory is discovered, he gives the Science Ninja Team the order to destroy it.

A secret base. In order to resist their terrible enemy, Nambu thinks about a base for the Science Ninja Team. But fearing enemy intervention, he gives the Ninja Team orders to fly a patrol at Point G in the southern Pacific Ocean. Following orders not to intervene there, the God Phoenix leaves a smoke screen and flees when it encounters a sea anemone mecha. That night, Jinpei is with the other four team members, but he is not tired at all. He takes the G-4 and dives to the bottom of the sea. Children in the park had told him that G-4's popularity is the lowest of all the team members, and he intends on gaining their favour by being the best. Despite the worries of the other team members, he wanders around the sea bottom searching for the mecha. He never notices that he is being tailed by the mecha he seeks.

In the deep black sky the blue-white moon is shining. Suddenly, a meteorite falls down to Earth. According to analysis, the meteorite has the same composition as the moon. So Ken proposes approaching the moon in the God Phoenix to investigate. Approaching the moon, the God Phoenix encounters a swarm of meteorites heading for Earth. Ken discovers a wrapped up body in the middle of the swarm and, because this is not a meteorite he attacks. But the Bird Missiles have no effect. The body falls to the Earth, becomes a Scorpion Mecha and attacks an oil refinery.

Suddenly, a whole city has lost power. Ken, in his Cessna, is thinking about an anomaly in the power plant when he gets a message from Nambu that the nuclear power plant has been attacked by a large group of ants. The Science Ninja Team goes to the site in question, but since the missiles would have hardly any effect on the tiny groups, they wash them away by breaking a nearby dam and using the force of the water. Upon analysing an ant they brought back, they learn that it's a finely and precisely manufactured robot.

While flying, Ken is surprised to encounter the plane of the Red Impulse commander. He pursues him, but Red Impulse gets away using some superb flying technique; Ken longs to be able to use similar techniques. The Science Ninja Team gets order to guard the super powerful plane "Blue Hawk", pride of the country Toritan. But the crew of the plane has been killed before take-off and has been replaced with Galactor members. Nambu learns of this situation after take-off. He mobilizes Red Impulse in order to protect the Science Ninja Team from the Blue Hawk, since it is more powerful than the God Phoenix. The God Phoenix continues to accompany the Blue Hawk without knowing the situation onboard. Red Impulse appears, attacking the Blue Hawk and, after shooting a timebomb into it, disappears again. Ken sees that and firmly believes that Red Impulse is actually an enemy. Ignoring Nambu who wants to stop him, he pursues Red Impulse alone in the G-1. While Ken is away, the other four members get abducted and taken to a base located in a volcano. Ken however follows Red Impulse, who in turn is following the signal emitted by the time bomb. They arrive together and save the team just before they're executed. Nambu tells them that Red Impulse is a friend battling on their side. The G-1 and the Red Impulse plane fly through the sky wing-to-wing, reminiscent of bird parents flying with their children. Nobody at the time knows the meaning of the tear appearing in the Red Impulse commander's eye.

The world's raw material for sugar gets stolen by the Galactor mecha Ibukuron, and the world emergency sugar is getting very low. Ryu and Jinpei rush out into the street to buy candies. Just then, they get the order from Nambu to move out in order to follow Ibukuron and find the secret base. During the pursuit, the God Phoenix gets drawn toward the mecha by its strong magnetic force it uses to suck in the raw materials. Ken uses this force to sneak into the interior of the mecha, along with Joe and Ryu.

A ISO constructed storage lake, which is part of a plan to make the desert fertile, disappears. The Science Ninja Team flies to Africa to investigate. An Elder there tells them the legend of the moving red sand. It is said that the red sand burns forever and that it can make civilisations grow, as well as destroy them. Ken asks the Elder about the sand's secret, but the Elder doesn't tell anything. Jinpei, following the Elder who's about to get abducted by Galactor, finds a pendant. The red sand contained in its interior is sent to Nambu and the analysis reveals that it's a new sort of bacteria and also a previously undiscovered powerful energy source. It has a thousand times the force of uranium and, if water is added, splits up and causes a big explosion. Because Galactor is looking for the red sand, a lion ant mecha changes the lake's location via an underground channel. The God Phoenix dives deep underground, discovers the caves used by the mecha and sneaks into the base they discover. But Galactor learns of the Science Ninja Team's arrival and they shoot the Elder after he reveals the secret. They head to the location where the red sand is locked up, one step ahead of the Science Ninja Team. Before dying, the Elder tells the Science Ninja Team the location as well. The God Phoenix gets there too late, the red sand is already stolen by the mecha. As a last resort, the God Phoenix turns toward the mecha as the Fiery Phoenix. As the red sand is touched by the flames, Galactor's high ambitions are burned, together with the sand.

It is reported that all kind of nuclear ships (cruise ships, submarines, battle ships etc) are disappearing. It is the deed of the Galactor mecha Icecander, aiming at nuclear energy. While investigating these incidents, the Science Ninja Team gets a message that a suspicious iceberg is moving forward against the current of the sea. The God Phoenix follows the iceberg, going to the north pole, where they discover a base in the middle of icebergs. Ken and Jun sneak into the base.

The town "Ghost City" has been destroyed 10 years earlier by environmental pollution. Communication with an investigation team sending data from there is lost. The Science Ninja Team goes there in the God Phoenix, which uses a soft skin (membrane) to protect it against the pollution. But as soon as they enter the city, they meet a Galactor attack. As it turns out, there's a base here. Nambu orders the U.N. military forces to attack. It seems everything is cleared after the attack. In reality however, a jellyfish lens created by Sosai X continues to grow at the bottom of the sea near the city. It uses the polluted sea water as its amniotic fluid.

The latest ISO weapon factory is used by Galactor and manufactures Mekanika. It's a machine which, according to the plan on a microfilm, can change its form constantly. The Science Ninja Team follows Mekanika. But when they lose sight of it, they continue searching individually before meeting in Nambu's house. While searching a tunnel where they lost sight of Mekanika, Jinpei discovers a base through a hole in the surface and sneaks into it. While trying to destroy the base, he finds a micro cassette. Judging from the behaviour of the Galactor members, this cassette seems to be very important and Jinpei takes it with him while fleeing. It contains the plans needed to change the form of Mekanika. Nambu makes a new plan, based off the cassette, and instructs the Science Ninja Team how to install this plan in Mekanika.

X, intending on using the strong destructive tendencies of humans, especially children, releases Kabutoron in the city. It destroys things using the children's brain waves. The children are happy when they find big stag beetles in one of the open areas, something which rarely happens in town. Also Jinpei finds one of the bugs and brings it home. In that night, each of the children's stag beetles grow large and they pull the children inside their bodies, fly out the room and start to destroy the city. While flying, Ken discovers how Kabutoron attacks a nuclear plant. But since Jinpei is missing, the God Phoenix cannot take off.

A huge whale keeps attacking harbours. While investigating a group of whales, the Science Ninja Team discovers a huge whale heading for this group. The huge whales fires a rocket aiming for the God Phoenix and flees, pushing aside the other whales. In reality, it's a Galactor submarine camouflaged as a whale. They want to follow the huge whale submarine, but, in order to save a young whale under attack by orcas, the G4 flies away. During all this, the submarine gets away. Nambu reproves them because of their squeamishness and puts a transmitter on the small whale so that he can help in the search for the big whale. The God Phoenix goes to the Arctic Circle, following the small whale. In order to search for the base, Ken and Joe leave the God Phoenix and encounter two men who introduce themselves as forest-keepers, but are then attacked from behind. Ken is baffled. Joe says that this is Galactor's trick and that his parents got murdered by the very same trick.

The Ruman Kingdom is known as the Gambling Kingdom. Galactor, guaranteeing the king's position, is channeling millions in riches out of the country. His highness Prince Luga's heart is torn by the people moaning with the high taxes imposed by the kingdom. So he contacts the ISO and offers to hand over a microfilm containing the location of the Galactor bases and headquarters to them. He does this knowing that it's against his father the king's, orders. In order to lay their hand son the film, the Science Ninja Team takes part in a race sponsored by the prince in which everybody can participate. But the encounter obstacles set by Galactor, who know the prince's plans. They're lured, together with the prince, into the base located in the interior of the kingdom.

A Galactor mole mecha appears. The Science Ninja Team is contacted and starts to meet, but on the way there, Joe wants to save a small dog beside his mother, who was killed in the attack. Joe suffers a rocket attack. The mecha starts attacking the God Phoenix as well, but, since it gets weak in the sun, it has to withdraw at dawn. In the examination it becomes known that Joe got hit in the head by a fragment of the rocket. Since it's a very dangerous area an operation is impossible. Also the attempt in the high speed centrifuge fails. Then a message arrives saying that the mecha has appeared again.

A horse owned by a doctor who is an authority in the area of cyborgs, participates and wins with an astonishing performance at the world-famous horse grand prix. When Nambu sees this video, he guesses that this horse is a cyborg. He orders the Science Ninja Team to guard the Doctor so that his astonishing cyborg technique is not abused. But when Ken and the others arrive, it's already too late. Only one Galactor badge has been left behind and the Doctor has vanished. Dr. Henjinman has been brought to the base where he recognizes X's real face. He threatens X, saying that he will reveal his secret if he is not made X's representative. X reluctantly agrees.

A uranium mining factory at the bottom of the sea is attacked by the mecha "Kingdragon". Since a guard vessel with much more power than the God Phoenix was beaten during the attack, Nambu does not order the Science Ninja Team deployed. But Ken disobeys Nambu's orders and goes to face the mecha in the God Phoenix. But the God Phoenix is no match against the enemy and even their trump card, the firebird, is beaten by the much higher temperatures. Nambu orders the Red Impulse group to attack the mecha, but the Red Impulse commander believes that Ken should face the enemy again and refuses Nambu's order. So Nambu comes up with another plan. He wants to install a cooling device in the God Phoenix, which is then supposed to react with a minus bomb to be installed in the interior of the mecha to freezing the enemy. Knowing this will be very dangerous, Ken applies for the job of installing the minus bomb.

From the cellar of a bowling alley, the "Mecha Ball" appears and starts to destroy the city. Because of the Mecha Ball's simple structure, an attack is futile since there is no weak point. Opposing his four eager teammates, Ken decides not to go out, saying that if they attack without a chance for winning, they will only die a useless death. At the same time, Ken watches Jinpei move a pachinko ball with a magnet and gets an idea how to defeat the mecha. When Nambu hears Ken's proposal, he immediately builds a huge electrical magnet in the middle of the alps and decides that the God Phoenix must lure the mecha there.

Scientists from the ISO headquarters are murdered one after the other and Nambu orders the Science Ninja Team to act as bodyguards. The Science Ninja Team separate for their guard duty. During Ken's guard, he surprisingly meets Galactor's Ninja Blackbirds and follows them, but loses sight of them near an amusement park. At the same time, Jun and Jinpei are attacked by a Neon Giant which appeared accompanied by the sounds of a flute. In order to let the scientist escape, they offer themselves as bait, but fall off the street. Jun reports that the Neon Giant resembles the Indian statue standing before the amusement park where the Black Birds vanished. Because of that, the Science Ninja Team waits for the night and sneaks into the park to start investigating.

An ISO volcanic research center is attacked. The God Phoenix, starting the investigation, is surprised by the Magma Giant and escapes into the sea where the Giant cannot follow it. When Joe says that the Magma Giant's face resembles the face of Jesus Christ sculptured into a steep slope in the national park, the Science Ninja Team goes there to investigate. A girl climbing the Jesus Christ sculpture is suspected to be a Galactor agent by Joe and questioned, but she answers that she's here to sculpture the statue, continuing the tradition of her family in the third generation. Together with the girl they go into the cave found in the steep slope and discover a base. The Jesus Christ face sculpted in the slope, is plunged into lava seething in the interior of the base and comes out as the Magma Giant. Seeing this, Ken calls the God Phoenix. At the top of the base, there's a special glas which is actually at the bottom of a sea. The sea is used as a lense to heat the magma, using the sunlight. With a rocket, they break the glas and thus destroy the base. When a message comes in from Nambu that the Magma Giant is heading towards a city, the Science Ninja Team split up in their individual machines and lure the Magma Giant towards the sea. The Magma Giant cannot resist and steps into the sea. Through the sea water he's instantly cooled and becomes a black piece of rock, standing still. The girl then gets her chisel to begin sculpting again.

ISO ships are attacked one after the other by Galactor's black ray. And because Ryu is napping in the God Phoenix, he cannot be mobilized. Ryu feels responsible and gives Nambu his bracelet back, while shaking off his teammates who want to stop him. He then goes back to the fishing-village where he was born. During this time the fishing areas in the village become polluted through unknown causes. Since Ryu's father is the co-operative head, is blamed by the village people. Ryu tells his father to ask Nambu to analyse the sea water. In the analysis, a matter is found which results from a process to produce metal. Nambu thinks it's Galactor's deed and arrives in the fishing village with the Science Ninja Team.

The ISO gets a message from Lucy, one of the executives at Galactor, that she wants to reveal the location of their headquarters in exchange for $ 10 billion. Therefore they contact Lucy by having Joe team up with her in the world customer car endurance race across Africa. The other 4 team members are going to act as guards for their scout. After Joe gets into the car, he expects the information immediately, but Lucy says it's not possible until the rally is over. On the way, they are attacked by mechas camouflaged as animals. It is Galactor who have come to know of Lucy's treason. But with Ken and the other's help, they escape the attacks and continue the rally. As they approach the finish line, Lucy asks her old friend Joe whether they don't want to team up and take over Galactor. Evading all kind of obstacles, the team of Lucy and Joe wins the race and gets $ 100'000 in prize money. In the tea room, Joe demands that Lucy gives him the information as offered. When Lucy tries to answer, she suddenly starts to move strangely and finally breaks through a wall and falls to the ground where she explodes. She was a cyborg manufactured by Galactor, and a radio signal emitted by X caused her to self destruct. Joe is taken aback by Lucy who is now nothing more than a pile of iron fragments. His anger towards Galactor is ignited again.

Children keep dissolving into thin air. Even the members of the Science Ninja Team become eye witnesses to one of the disappearances. Ken follows some tire tracks on the ground and enters a mirror maze. There he discovers some snail mechas, but they become transparent and disappear. Galactor is collecting children with strong brain waves in order to produce the brain wave monster Alphagila. The monster reads the secrets of the ISO in its institutions, and then destroys them. Nambu enhances Jun's brain waves for a while and makes her pose as a bait. The Science Ninja Team locates her radio signal, sneaks into the base beneath the mirror maze and saves the children.

Jinpei and Ryu visit the Shirayuki orphanage where Jinpei grew up, in order to play with friends. The children beg them to take them to watch some kickboxing. At the same time, in a volcanic area, strange things are happening. Ken and the other two go to investigate, but don't find anything extraordinary. After watching the fight, the children go to ask the winner, Galack X, for an autograph. They learn however that he was trained with deadly weapons in his boxing gloves. They are caught by the female assistant and taken away. Ryu, following Galack X by Jinpei's request, battles with Galack X, but gets hurt. He contacts Ken and the others.

A water shortage is occurring everywhere. As if to pursue the beaten enemy, an invisible enemy continues to pound, destroying dams and water tanks. The Earth is put into a grave situation. The God Phoenix is mobilized and discovers the flying mecha Kamisoral which has become a white shadow. Merely flying past it causes great damage and missiles are useless since they can be cut apart by the mecha's sickle. The Science Ninja Team somehow manages to escape and report to Nambu. During this time, an announcement from Katse is received saying that tomorrow will be the last day for mankind.

Nambu's car is attacked by Galactor. But because of Joe, who seems to remember the Devil Star's rose bomb, they escape by a hair's breadth. Everybody wants to fully concentrate upon protecting Nambu since he's targeted. But Joe cannot agree with them and leaves the villa. In order to control his anger, Joe runs his car around a racetrack. When his parents were murdered, he too suffered a lethal wound by a rose bomb. His memories revive and he thinks of revenge. Just then, he has to save a woman from an accident on the track. Before parting, they make an appointment to race on the track together the following day.

Receiving a warning from Galactor, the Science Ninja Team mixes with the other citizens and starts to investigate. But thinking this might be a Galactor trap, they take off their bracelets and split up in the city.

The Science Ninja Team doesn't know where Jun and Jinpei are, and Gezora starts to attack. But with two of them missing, scoring is difficult for the team.

Strange radio waves attack people together with an aurora. Afterwards they run amuck and cause grave accidents. While fishing, Ryu is also bathed in these radio waves. Because Ryu's speech and behaviour are strange after he comes back to the base, an investigation is conducted. It results that Ryu's brain waves are like those of a cat. Additionally, Nambu is touched by those radio waves as well. In a rage, he tries to activate the switch for the self-destruct mechanism of Crescent Coral. Joe punches him out.

In the country Doria, oil springs have been discovered. A battle has started between the King, keen on the mining rights, and the Prince, who's on the side of the poor, revolting people. It has become a civil war. Now there's also a never sleeping force, intent on making this into a world war. The King, in a disadvantageous situation in this war, asks the Science Ninja Team for help. The God Phoenix sneaks into the country in firebird mode. Ken contacts Prince Ali and convinces him to talk one more time with his father, the King. Together they go to the palace. But the King's answer is a volley of bullets, aimed at the prince and his companions. Ken stops the Prince who wants to attack the King. They both are dropped through a hole in the floor into a subterranean prison, where they find the skeleton of the true King. Ken tells the God Phoenix to come and get them, thus escaping.

An ISO research ship is attacked and data regarding uranium resources on the bottom of the sea is lost along with it. In the middle of the investigation, the Science Ninja Team discovers three persons, a father and his two sons, floating on the sea. They say they witnessed the occurence while fishing. But in the village they live, the brothers Taro and Jiro and their father have the reputation of being liars. Nobody wants to listen to their testimony that they saw an apparition of a crawfish and a moving lighthouse. Ken discovers that the squid the family fished out is a rocket. The Science Ninja Team decides to have a look at the lighthouse.

Dr. Miwa is researching whether the surface of the Sanjo Lake, frozen over the whole year, can be used to produce strong energy from the sun, instead of using polarization glas. Now he has gone missing. He had questions because this year the lake wasn't frozen over and seemed to have started an investigation. Nambu orders the Science Ninja Team to look for him since he fears the misuse of the Doctor's research, but also because the Doctor is his friend. The Science Ninja Team, led by the Doctor's pet Taro who was able to get to Nambu with a camera, heads towards the snowy mountains. There they discover a Galactor base. The Science Ninja Team and Taro are tricked by the Doctor's reflection. Taro is washed away by water falling from the ceiling of the base where the surface of the lake is located. The Science Ninja Team is locked up by walls made of reinforced glass.

As part of the Mantle plan, a pollution-free city is constructed in the desert. Nambu and the Science Ninja Team have come into the city for the inauguration. In the middle of the parade, a man who introduces himself as the archaeologist Dr. Mukashiski is distributing leaflets for a dinosaur exhibition. That night, the city is attacked by dinosaurs, and Ken sneaks into the dinosaur exhibition from Dr. Mukashiski. It turns out to be a jungle from the dinosaur period. Ken is caught by ivy made of metal and can escape into a subterranean sewer, but his bracelet is taken away this time. The Doctor takes the bracelet and, in order to make this is own merit, hides it.

Outside of Earth's atmosphere, a Devilstar ship appears. Spores of the Jigokiller plant are released towards Earth by Katse's hand.

Jinpei is lost in mourning in Jun's empty shop. Elsewhere, Nambu is absorbed with the research on the Jigokiller plants.