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. Ken discovers the spaceship's capsule inside the aircraft carrier, but the astronauts have been taken hostage. Ken is caught then too. In reality however, the pilots have already been murdered. Showing them as if they were still alive has been a trap. Jinpei has sneaked into the aircraft carrier following Ken on Joe's orders. He is able to rescue Ken as he is being led underground. The two of them collect the device and escape, destroying the computer in the aircraft carrier. The commander of the carrier gets blamed by Katse, and he gets into the head of the Turtleking to hurl himself at the God Phoenix. But due to Ken's quick thinking, the God Phoenix becomes the Firebird and the flames consume everything.

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. He meets Makoto's father, who miraculously survived the crash. But it's Katse in disguise. Katse battles with Ken and escapes. Makoto blames Ken for torturing his father and Ken promises him to bring back his father whereupon he gets the pin hiding the Uranless. The giant mummy appears at the airport and Ken is able to defeat it by firing the Uranless into it. But Makoto watches Katse, still in the guise of his father, flee in an escape rocket. He accuses Ken of breaking his promise to bring his father back. Ken accepts Makoto's hate silently since he lost his father ten years before in a similar way and has had the same thoughts - namely that his father would return some day.

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. In an investigation it has been calculated which resources the mecha will most likely attack next, and the God Phoenix encounters the mecha there. Inside, Ken wants to let Naomi avenge her father and asks Nambu for permission to fire the bird missiles. Nambu doesn't give permission, but Ken ignores him and tells Naomi to fire the bird missiles anyway. Naomi hesitates to press the firing button, and Ken takes Naomi's hand and makes her fire the missiles. At the director's grave, Ken hands his bracelet to Nambu. He says he wants to take the responsibility for making Naomi press the firing button without permission and resign from the team. However, Nambu says that Ken is needed for world peace and Naomi promises not to reveal his true identity.

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. But when Joe says that all the ships are actually battleships, Ken gets suspicious and has the God Phoenix surface. There's fog everywhere on the surface. From the middle of the fog, a ghost fleet attacks them, but the Science Ninja Team guess correctly that the fog is man-made. They destroy the device creating the fog, but from the ghost fleet appear countless disks which attack them using light rays. The Science Ninja Team has to fight a hard battle. Just when all the missiles are used up and they don't know what to do, three red planes appear and shoot down the enemy machines using superior flying techniques. The commander of the fighter plane unit introduces himself to the baffled Science Ninja Team as "Red Impulse". He then flies away, leaving the words "We'll meet again" behind.

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. While Ken and the other create a lot of confusion in the interior of the base, Joe goes looking for the gold bars. He learns that a missile is about to be fired at the God Phoenix when it is detected by the surveillance cameras. He contacts Ryu in the God Phoenix, right away. Ryu, who is always merely on stand-by, is taking a nap, though manages to evade the missile by a hair's breadth. With Joe's guidance they store the stolen gold bars in the God Phoenix's interior. Ken and the others are contacted and escape from the base. The Galactor base and all its inhabitants are blown up because they didn't manage to prevent the gold bars being stolen back.

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. While the Science Ninja Team conducts a search with the God Phoenix in a mining area, they detect a huge mine. When they discover that this is where Galactor's secret factory is located, they sneak into it. By the end of the battle, they have succeeded in destroying the computer and the nuclear reactor. They try to make their getaway in the God Phoenix, but are caught by the strong magnetic attraction of the mine. They switch to jet propulsion and escape by a hair's breadth, leaving the exploding factory behind them.

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. Jinpei finds what seems to be a base under construction, but is caught by the mecha. He contacts Ken, but the base is blown up before his eyes. The mecha is destroyed by the God Phoenix and Katse gets away again. Jinpei wails that the base has been blown up because of his own egoistic actions, but Nambu tells him that the destroyed base was only a decoy. The Science Ninja Team had been the bait to attract the enemy's attention. The God Phoenix is flying high in the sky. Deep below stretches a crescent shaped coral reef. Below the reef hides the base which is capable of changing its location.

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. Following Nambu's instructions from Earth to find the source of the radio waves steering the mecha and the meteorites, Ken asks Jun to trace the signal they detected while the mecha was on its way to Earth. The Science Ninja Team find the carrier sending out the control signal and leave Ryu behind in the God Phoenix while they sneak into it. They question the commander, but he doesn't reveal anything. Joe loses his patience and fires carelessly into the control panels with a machine gun. Shortly after the Science Ninja Team escapes, the meteorites hit the carrier because the computer has been destroyed. Meanwhile on Earth, the Red Impulse squad reports that the now unguided scorpion mecha has been destroyed.

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. The robot ant gets repaired and, following its control signal, returns to its base. It is followed by Ryu in the God Phoenix in the sky and by the other four on the ground. They soon discover huge ant-hills, and end up in a huge ant cave when they try to sneak in. Katse is waiting for them where they fall and captures them in a dome made of reinforced glas. The air is about to run out and they don't know what to do, but in the end barely escape by using a bomb. In the meantime, swarms of ants have attacked the streets, but the Red Impulse squad exterminates them with flamethrowers. At this time, Katse lets a huge ant mecha take off. Red Impulse and the God Phoenix drive the ant mecha into an underwater tunnel. Collecting the sunlight with a mirror built into its nose, the God Phoenix burns everything with a strong heat ray. But Katse gets away again.

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. However, the interior turns out to be a sugar factory and the three team members get sucked into the production process. They almost fall into a huge cooking pot filled with seething raw material, but somehow manage to escape. But then they enter a centrifuge and are rendered completely helpless. Meanwhile, Ibukuron has arrived at the base in a snow mountain and Jun and Jinpei sneak into its nuclear energy chamber. They turn off the power source, but get caught by the enemy. With the power turned off, Ken and the others can escape and arrive to rescue them. Just before escaping, Jun installs a time bomb and, as a result, the base disappears in the middle of an avalanche. The Science Ninja Team distributes the sugar, which they won back from Ibukuron, in a park. The children are now happy again.

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. In the base, while they are trying to take out the nuclear reactor, an operation is performed, designed to convert the crew and the passengers of the ships into Galactor members. With this strategy, Galactor wants to gain nuclear energy AND new members at the same time. Just at this moment, Katse wants to perform the operation on a small girl, passenger on one of the cruise ships. Ken and Jun invade the room and stop the operation, but Katse locks them up and leaves a time bomb in the room. In this instance, an old man in a wheelchair, who was on the same ship as the little girl, takes the time bomb in his arms and sacrifices himself, saving the others from the explosion. Ken and the others exit the operation room. First they free the abducted passengers and let them get back on board, then they blow up the base and escape. The Icecander pursues them, but the God Phoenix encounters it using the fiery phoenix and the mecha goes up in flames.

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. After finishing its growth, the jellyfish lens which turns the sunlight into energy a few hundred times stronger, completely destroys fighter planes from the U.N. forces. It then starts to attack the cities on earth. The God Phoenix dives into the sea near the city and discovers the base and the hiding jellyfish lense. They attack with missiles, but even though they destroy the base, the jellyfish lense flies out of the sea, pursuing the God Phoenix. The membrane protecting the God Phoenix is peeled off and puts it in a difficult situation. Just then, the Red Impulse group gets Nambu's instructions that in order to dissipate the poisonous gas the jellyfish lense breathes, they should throw high pressure oxygen at it. Protected by the Red Impulse machines, Ken flies they fiery phoenix into the jellyfish lense. The high pressure oxygen goes up in flames and the jellyfish lense burns to ashes on the surface of the sea.

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. As Mekanika transforms, there's a chink between the different parts of the casing. Ken sneaks into Mekanika through one of those chinks and wants to insert Nambu's cassette into the computer, but gets into a melee with Katse who was in the pilot's seat. Ken dives under Katse's arm and somehow manages to insert the cassette. Mekanika, according to Nambu's plan, transforms into a fair. When Katse sees that, he flees.

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. Ken transmutes into his G1 plane and uses his X-ray on Kabutoron. Because he sees a child in the interior, he ceases to attack. The four members of the Science Ninja Team shadow Kabutoron and discover a base hidden in an ancient ruin. In the interior of the base, an operation intending to remove the children's brain and install them into Kabutoron is about to begin. A drill is just touching Jinpei's head when he's saved by a hair's breadth by Ken and Jun. They save the other children with Joe's help. Ken and the others get into the God Phoenix. Bombed by Red Impulse, Kabutoron blows up together with the base.

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 Science Ninja Team discovers the base and sneaks into it. They learn that a group of submarines is about to leave and attack the harbours in the world. They install explosives in the base and in the submarines. But, in order to help the little whale who ended up in the base, Jinpei dives with him into the sea. The Science Ninja Team can't stop the operation at this point, and escapes leaving Jinpei. But after the explosion of the base and the submarines, they are contacted by Jinpei, saying that he was saved by the small whale, and everybody is very relieved.

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. Katse wants to force them into exchanging the film against the king's life. But the prince has already handed over the film to Ken. Katse gets angry and shoots the king. The prince, clinging to his father's body, cries very much. But he has now his duty towards the people of the kingdom. Katse wants to take back the film by force. In order to achieve this wants to cut open Jinpei's stomach, since he pretended to swallow down the film. After the ensuing brawl, Joe has Katse cornered and is about to take away his mask, but Katse get away again by a hair's breadth. Despite the fact that they saved the prince's life, the film, which cost a huge sacrifice, was burned as well.

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. The other four members are mobilized, but their thoughts remain with Joe. But because the G2 car does not meet up with them, the God Phoenix cannot use its normal powers. At that moment, Joe appears in the G-2. He's taken immediately into the God Phoenix, but while they are still thinking about the reunion, they are caught in the mecha's hand. The God Phoenix wants to escape its certain doom, but it's impossible. Joe presses the firing button for the rockets and blows up the mole mecha. The God Phoenix is caught in the resulting shock wave and is thrown away rotating heavily, but with Ryu's steering capabilities they can recover. The resulting jolt gets the fragment out of Joe's head and he escapes alive.

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. The Doctor's cyborg horses attack a meadow. The Science Ninja Team pursue them and sneak into the base. Inside, they find the doctor standing before X to reveal his face, just as he wanted. The doctor falls down as he's hit by a light rays projected by X when Katse pressed a button. Katse orders the horses to attack the city and flees. The Science Ninja Team escapes and blows up the base. Dying, the doctor tells them to press the buttons on the horses' backs. After the Science Ninja Teams has pressed the buttons on eac of the horses, he activates the self destruct mechanism of the horses and silently dies.

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. Hiding in a swarm of tuna, Ken sneaks into the mecha. He succeeds in placing the bomb, but he has no more time to escape as the mecha starts to freeze from the icy firebird. The Science Ninja Team is worried and wondering about Ken, when he suddenly appears in front of them from a crack in the mecha, like an immortal bird.

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. But with the mecha lured halfway to its destination, it changes its course to an international nuclear plant. Ken wants to get into the mecha himself and steer it towards the magnet. Joe wants to stop him, but Ken convinces him and flies away from the God Phoenix. Getting in the mecha alone, Ken defeats the Galactor members and changes the course of the mecha. He destroys the steering panel, making sure the course cannot be changed anymore. As Jun holds her breath and watches, the mecha ball is drawn towards the magnet and explodes. Ken's figure is reflected in the tear-filled eyes of the four teammates, similar to a bird flying in the sky.

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. Since Jun said that she heard the sounds of a flute, Ken follows a flutist who leads him into an underground base. It's Katse in disguise. Katse tells Ken that this night, Nambu will get attacked. Ken gets in contact with Joe and Ryu, telling them to hurry to Nambu's location, but he's caught in a pertinacious attack from the Black Birds. Before his eyes, Katse steers the Neon Giant with the flute's tune. When Jun and Jinpei intrude, Ken flings the flute away, and orders Jinpei to play on it. Through Jinpei's nonsensical tune, the Neon Giant overheats and explodes. The plan to asssasinate Nambu has failed.

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.