A shining object collides with the luxury liner Queen Margareth. A child with special chromosomes is abducted from the sinking ship. Governor X has returned and with the help of his scientific power the child grows very quickly. It is given the name of Gel Sadra and enters on the task of being the new Galactor leader. Soon, numerous scientists and soldiers begin to disappear. Elsewhere, Dr. Nambu has already predicted the counterattack of Galactor. He has had the Science Ninja Team resume their activities at their underwater carrier base G-Town, which capable of changing its location. The revived Science Ninja Team greets Getz as the new G-2 and is ordered by Nambu to investigate some ruins on Easton Island. But Getz is a member of the enemy forces. The ruins are a trap and Gel Sadra is waiting there. The Science Ninja Team ends up in the ruins facing an enemy robot in the form of a statue representing a deity, equipped with laser rays. It shoots at anything that moves.

.. and the team doesn't know what to do. But thanks to a bomb somebody installed in the robot statue it is destroyed, and the team sees Getz killed by a feather shuriken. They pursue a fleeing shadow which looks like Joe. But was it really Joe? Could he be alive? The shadow leads them to a secret Galactor base which uses the ruins of the shrine as camouflage. Galactor continues in its preparations to launch the missile. The Science Ninja Team wants to stop them and they get into their individual mechas The five of them start an all-out attack on the base. Because of the Ninja Team's attack, the Galactor operation ends in failure, but Ken's Eagle Sharp is wrapped in the explosion's flames and crashes in a forest. While losing consciousness, Ken faintly hears Joe's voice. When Ken regains consciousness, a man is standing before him. It's the former Galactor physician, Doctor Raphael. He tells them of his childhood, revealing his hate for Galactor. Then Jinpei notices that Raphael's shadow is similar to Joe's. Dr. Raphael tells them that it was him who saved them from Galactor.

Somebody sneaks into Galactor's Headquarters and a plan to build a huge base in San Frangeles is relayed to the Science Ninja Team. Ken and the others are baffled at the voice of the communication. It sounds exactly like Joe's. Elsewhere, Galactor has a corps of knights, clad in black armour made of a special Sigma lightray-strengthened steel, sneak in places to steal nuclear energy. The plan is to have them destroy the city of San Frangeles while the base is still being completed. The Black Knights are actually internationally wanted criminals. Since the Science Ninja Team has been told that the escapees have secretly built a town, they go to the ruins of the prison on Alamo Island by San Frangeles. Jinpei is given precise instructions by a voice that sounds like Joe's and the Ninja Team discovers an enemy base that is still being constructed on the bottom of the sea. They sneak into it and install a time bomb. However, they are captured by Gel Sadra. The Science Ninja Team dares to try the Tornado Fighter to escape. The base explodes and they end up floating on the sea, from where they are again rescued by a mysterious person.

In the country Amelia, between the cities New Jork and Scratton, there's the Dera Desert. Below that desert, Galactor is building a scecret base which is supposed to become a very important military strong point. But because they have rushed its completion, a huge explosions occurs and triggers a 9.2 magnitude earthquake in the area. The two cities get into a very critical situation. In order to find out what is happening, the team launches a sensor-equipped rocket drill into the Earth. The data is sent to the New God Phoenix and analyzed by Nambu. However, after the launch, the team is ambushed by Galactor and, yet again, the mysterious person saves them. The only way to save the cities is to dive under the desert in the Condor Attacker, since it can take the pressure. Through the explosive power of the Fire Targetter, which is equipped with the ultra powerful Tektay explosive, the mantle convection can be calmed down. However, there's no G-2 to pilot the attacker. Just at this moment, Condor Joe finally appears alive before the Science Ninja Team. Then Ken and the others face the mecha which has appeared, while Joe accomplishes his task perfectly.

In the underdeveloped jungle country Fruginia, a village is destroyed by cavemen. Soon after, Neanderthal cavemen attack the country of Amehon, which is 200 kilometers away. They are immigrants from Fruginia who have been transformed by Galactor with the help of a special liquid. Among them is Toro, the father of young Shiro, whom Ken and the others met earlier by coincidence. Galactor plans to transform the all of humankind into cavemen, and, wants to pour chemicals into the water reservoirs to achieve this. However, the Science Ninja Team stops them. Galactor then releases a demonic energy which makes the cavemen violent and dangerous. They start to destroy the city. The mecha controlling the energy shoots down the God Phoenix. The team gets into the city, but can't confront the cavemen because they're humans. But when Toro is coincidentally reunited with his son and refuses to destroy things, the demonic energy flows backwards into the mecha. The enemy mecha starts moving by itself and ends up exploding. Consequently, the love of the united father and son has smashed the Galactor plans.

South of the Road Island, accidents involving ships and airplanes keep happening. There are no clear messages and the cause of the accidents is unknown. The Science Ninja Team suspects that the experimental city in the middle of that island, Egypt, has something to do with it. The city has been built in order to collect the pyramid power, which is impossible to control when rising. Jinpei goes to Egypt alone to investigate. There he meets Yukari, the daughter of Dr. Sugata, the leader of the development of the pyramid system and the city. However, Sugata has asked Galactor to help him in the construction of Egypt, despite knowing they are evil. Soon after completion of the system, a huge pyramid shows up that had earlier been hidden in the volcano of the island. It sucks the energy out of the smaller pyramids. Then, the city is destroyed together with all the employees and the VIPs visiting the city for the inauguration of the system. Dr. Sugata's daughter is there too and is almost killed. When seeing this, Sugata asks Gel Sadra for help. When she refuses, he notices for the first time that he may have made a mistake. Following his suggestion, the Science Ninja Team uses the Firebird Shadow Separation, creating multiple firebirds and aligning them into a huge pyramid larger than the one from the enemy. They succeed in destroying the enemy pyramid this way.

Sosai X's voice resounds: "Did you see that, Gel Sadra? This is the space plant Redda which I manufactured". Through Governor X's mysterious extraterrestrial science, the artificial space plant Redda is born. By coincidence, a boy named Harry finds one seed which has been blown away, and takes it back home. Sprouting, Redda grows very quickly and attacks Jinpei, who has come to visit Harry. But suddenly, Redda withers when it is eaten at by huge swallow-tails caterpillars. Soon, the seed is spread out by Galactor in the city of Newshington. The city is converted into a jungle. But since Reddy is neither hurt by fire nor by blades, Jinpei proposes using its natural enemy, the swallow-tail caterpillars. The caterpillars are collected immediately and spread out in the city. Through this measure, Redda suffers a total defeat due to this measure. The Science Ninja Team also destroys the Galactor base which was still under construction. However, after eating Redda, the swallow-tails grow very quickly and soon end their short lifespan.

A dark Galactor satellite keeps stealing space satellites and destroying them. It can absorb radiowaves, infrared waves and light, thus it is able to evade any radar. First a satellite investigating Mars disappears, then a communication satellite, then a space ferry and finally a weather observation satellite. Galactor wants to have the hindering Earth satellites out of the way so they can attack the sun with a long range beam cannon from their base on the back side of the moon. Jun and Jinpei board an observation satellite on Nambu's orders to find out who really is behind all this. However, the satellite is attacked, and Jinpei ends up falling into the enemy's hand. Additionally, a satellite to detect new raw material resources is attacked and the Saturn Rubin is stolen. It is said to let the power of the beam cannon increase. Joe uses the small space ship, Swanboat and gets into the dark fortress through the garbage disposal opening. He fails at the first try however, since the Swanboat was defective, and only succeeds when trying again. He detects the enemy base on the moon. The Science Ninja Team sneaks into that base, following the dark fortress. Joe saves Jinpei who had become a hostage. Afterwards, they blow up the base. The dark fortress escapes for a time, but they smash it with the Firebird.

Gel Sadra plans to destroy the Science Ninja Team with the Supermissile "Sea Tiger", from which it is supposedly impossible to escape, even if detected. However, Governor X loses his patience because of the many previous failures and wants to rebuke Gel Sadra for her arrogance. "Don't you think you take the Science Ninja Team too lightly? Berg Katse has fallen because of this as well". Gel Sadra answers: "No, that may seem so because I always have the self-confidence to defeat them." X enumerates the many times that Berg Katse failed. Galactor was very proud of its former scientific power, but all the mechas it constructed were no match for the Science Ninja Team's wits and courage... But Gel Sadra's arrogance doesn't diminish, even after she has to hear all this. With the Galactor North Pol base before its eyes, the God Phoenix is caught in the magnetic light rays of Sea Tiger. Joe completes a torn wiring circuit with his own body. Doing this, he allows the team to use the Firebird. As a result, they destroy Sea Tiger, the enemy base and foil Gel Sadra at the same time. Nevertheless, she answers to Governor X: "In these unsecure times, failure is the base for success".

Suddenly, the islands in the South Pacific Ocean are surprised by strange weather. Tens of thousands of people freeze to death because of the wind, snow and icy cold. This is caused by Galactor using the Earth's magnetic field to manipulate the Van Allen belt. In the middle of a magnetic storm, Ryu is sent to do some solo investigation in his Horned Tank, but he is dragged along by the ocean currents and propelled onto the beach of a lone island. There he happens to meet an old man named Rokko who breeds sharks. Ryu learns from Rokko that there is a Galactor base operating an antimagnetic ray canon in the coral reef in the ocean in front of the island. Ken and the others hurry there and together with Ryu they attack the Galactor coral base. They leave Rokko behind who is dying because of the cold weather. But since Galactor is using a special magnetic field with only one pole, their ray cannon disables all the functions of the God Phoenix. However, a harpoon they received from Rokko saves them from this critical situation, since the harpoon is not affected by any magnetic field. The Science Ninja Team smashes the enemy base, but they cannot save one old man.

Because of a defect in their car, Ken and Jinpei have a breakdown in the desert. A young girl named Julia takes them in her car. She tells them that she's on her way to the harbor to meet her older brother Jeff, who works as a secret guardsman at the ISO. But the three of them are attacked in the harbor by the Black Raven mecha corps and Julia ends up heavily injured. Governor X is searching for a new core element, Hypernium 600, which is said to be 600 times stronger than the old core element, Platonium. He starts blindly attacking the cities surrounding the ISO secret hangar in the Abata desert, with his raven mechas. Jeff learns that the next target for the attack is the city of Kinzu. The hospital that his younger sister has been taken to is located in this city. In order to hand over the Hypernium 600 to the enemy and save his sister, he goes to steal it. Ken goes to stop Jeff and to reclaim the Hypernium. Meanwhile, Joe and the rest of the team go to the enemy base with the God Phoenix. On their way there, they encounter the raven mechas which unite and form one huge bird, then attach themselves to the God Phoenix. Using "Bird Diving", the Ninja Team gets rid of the ravens attached to the hull, and destroy the enemy base with a missile. Ken forgives Jeff for his fault, and Julia stays alive.

Observatories and weather stations all over the world are attacked by UFOs. Additionally, authorities in the field of space communication are assassinated one after the other. Even Nambu can't guess the true intentions behind the incidents. In order to protect Dr. Kasshingu of the Irigutchi observatory, the Science Ninja Team goes to his whereabouts. But it's too late, they meet Dr. Kasshingu as he is already dying. The culprit is Galactor. Before dying, Dr. Kasshingu tells them that it was Dr. Raphael's Leapwave which made space communication possible. Upon hearing Dr. Raphael's name, Joe disappears from the sight of Ken and the others. Elsewhere Governor X is afraid of Dr. Raphael because he could unveil his secret. When X learns that Dr. Raphael is the only one able to send out the Leapwave, he goes berserk and orders Gel Sadra to pull the modulation waves of the Leapwave into his base and to reverse them. This way, he gives the nuclear missile launch systems a "go" order, with the aim of provoking a nuclear war. The whole world is plunged into a nuclear crisis without warning. Raphael has learned this and murmers "I am the one who called Sosai X from space. I have to take the responsibility." He then orders Joe to destroy the missiles of both parties with the antigravitational missile. A nuclear war is averted by a hair's breadth.

Joe has sneaked alone into a Galactor base, searching for Governor X. A mysterious girl named Cathy appears before him and tells him that Governor X has moved to the volcano Vesuvio. X has indeed moved to a base in the interior of that volcano, a base built by Berg Katse. X gets angry at a town built by people who are using the volcano's energy. He plans to destroy the city with missiles that will destroy the earth's crust. Magma streams into the subway system of the city. Elsewhere, Nambu who is the architects of the city, has a missile installed in the God Phoenix. This missile will solidify magma. He does this in order to save the city. However, they meet resistance from the enemy and the missile is wrecked. Joe intends to activate the magma solidifying device himself by throwing himself into the magma and pressing the switch. Cathy is a cyborg like Joe, and she has fallen in love with him.

A mysterious UFO flies over cities and mountainous regions all over the world. Additionally, airplane passengers who vanished half a year ago appear again, without memory. Because the spaceship has come to request to talk with humankind, the Science Ninja Team undertakes the task on a remote island in the South Sea. The person who exits the space craft is the famous Earth Defense Force pilot Major Borg, who was believed to be dead, killed in combat against Galactor. He says that when he was saved by that spaceship, Kentaro Washio was alive inside that ship. When Ken learns that his father, who sacrificed himself to save the Earth, is alive, he sways. He takes off in the G-1, following the UFO which took off after Borg exited. He sees his father through a window, but then crashes against a wall. Borg saves him and, led by Borg, Ken leaves in order to meet his father. Borg's son has been taken hostage by Galactor and Borg has been forced to set a trap for Ken.

Galactor's cruise missile crashes and explodes in a fishing village. Its inhabitants have disappeared. Ryu is sent to investigate and saves a girl named Yuka who is pursued by the villagers because they suspect her of arson. Yuka feels love at first sight for Ken, whom she meets because of the investigation. She tries to ensnare him. However, Ken is cold towards her, he does not understand such feelings. Elsewhere, Ryu has fallen in love with Yuka. He has watched everything and tries to comfort her. When she says that she lost a finger ring and that it fell into the sea, Ryu with his pure heart believes her immediately and jumps into the sea in order to search for it. He finds a pearl, and by coincidence, he also finds the cruise missile's memory chip that has sunk at the bottom of the sea. Ryu gives Yuka the pearl and hurries towards his comrades with the memory chip. In the analysis it results that the target of the missile was an observatory.

A Galactor traitor steals a secret micro file from a base and gets it to the ISO headquarters. In order to decode the file, Joe goes to the Ongurei Research Institute where they have some special decoding equipment. But there's an electronic transmitter attached to the file. Its signal is detected by Galactor and they proceed to attack Joe. Saved from the critical situation by Ken and the others, Joe hurries towards the research institute again. But a strong headache attacks him. He is blinded and falls towards a valley. "What's happening, this is not supposed to be happening to my body again" he thinks. While losing consciousness, Joe remembers his past, when he found out that his father was a Galactor member, when he died as a result from an old wound he got in his head, and when he was resurrected as a cyborg. Joe is saved by Jun and regains consciousness. The file is safe.

An experimental city named Seatoland that swims in the ocean, has been built by the ISO. It is attacked by a Galactor monster called Umiba, and faces total destruction. When this message is received, the Science Ninja Team is mobilized, but Dr. Siski, in charge of Seatoland, refuses to collaborate with them. Milly, the doctor's daughter, has been taken hostage by Galactor during the attack. The doctor himself has been intimidated and forced to collaborate with Galactor. The doctor finally tells Gel Sadra the equation which increases energy and allows the extremely powerful magnetic fields to be used. The doctor is then ordered to lure the Science Ninja Team into their deep sea base. Jun has overheard this by coincidence and knows now that her friend from childhood, Milly, is still alive and has become a Galactor hostage. Jun keeps these dangerous news away from Ken and the others. She sneaks into the deep sea base in the Marihole, together with the doctor.

A spaceship is being repaired by Jun. Jinpei releases a safety button because he is threatened by a gun, causing the spaceship to take off. The robot threatening Jinpei turns out to be a girl who introduces herself as Sachiko. Sachiko wants to meet her father, Tetsutaro Arimura, who works as research head at the Earth Investigation Station Moa. Following her wish, the ship makes a forced landing at the space station. But no one is there. While searching for Arimura, they coincidentally run into Galactor and get into a difficult situation. Galactor's goal is to steal data tapes of the Mantle energy and occupy the station. Using the two as hostages, they rob the Mantle energy data from Arimura. But the Science Ninja Team quickly arrives to rescue Jinpei and forces Galactor to retreat by shooting the artificial gravity device.

Communication with police and military forces in the highland of Oshia keeps getting cut off. Joe has been behaving strangle as of late, and as Ryu follows him, he disappears in that same spot. Ryu leaves behind the words "spiral galaxy!?". The Science Ninja Team thinks that all this is the deed of Galactor and starts an investigation in the Oshia region immediately. There, Governor X's new weapon, Galamoeba, is hidden and waiting. The Science Ninja Team tries to resist with the God Phoenix, but they are hauled inside the enemy mecha. There they are released into another dimension. The humans who disappeared were also in that other dimension. They had been brainwashed in order to become soldiers to build the solar shift plan. The Science Ninja Team is sentenced by Gel Sadra to vanish with the other dimension in twenty minutes. Ryu is floating around in this dimension and Joe rescues him with his car.

Tojo island, in the country Rizoto, sinks into the sea because of mysterious movements in the Earth's crust. Jun has gone to investigate the small islands in the vicinity and goes into a cave on one island. There she falls into a trap of a Galactor spy disguised as a survivor. The spy then disguises herself as Jun and penetrates G-Town. In the engineering room she installs a cloaking device. G-Town is being led towards a Galactor trap on the bottom of the sea. In reality, the spy is Eva, the daughter of Bill Douglas, who has developed the machinery of G-Town. She is being used by Galactor who told her the lie that her father was killed by the Science Ninja Team. Elsewhere, Jun has escaped from the enemy's prison. She attended the death of Bill Douglas there who was severely tortured. Jun goes back to G-Town and tells Eva what actually happened. Jun gives her a keepsake from her father.

Ken goes to the luxurious residence of his old friend Karl III, with whom he had lost contact. Karl is the successor to the leadership of a group of 300 enterprises in the whole world and is now organizing a meeting of the former pupils of the flying school which he and Ken attended. But Ken's heart is heavy because he has a task to verify whether or not the rumour that Karl wants to build an empire and conquer the world is true. But the rumour is true as Ken finds out when he's searching the house, whereby Lisa catches him. Together they find a secret passageway and hear Karl speaking to his troops. Karl is also secretly collaborating with Galactor. He offered them the Mantle Power-up Plan in exchange for weapons. Ken and Lisa are detected though. Karl tells Ken the truth and then wants to execute him and his fiance, Lisa (who also attended the flying school together with Ken and Karl). In that moment Gel Sadra appears before Karl and points a gun at him.

People keep collapsing everywhere. 20,000 humans die of unknown causes. Since radioactivity has been detected at the same time, the Science Ninja Team starts searching for its source. While investigating, Jinpei and Ryu encounter three boys and go with them to the Negiris plateau. The boys love UFOs and wanted to try to establish a contact with the extraterrestrials. They say they caught some strange radio waves while doing so. Following its source, Jinpei, Ryu and the boys arrive at Stonehenge. At that moment, a solarshifter appears out of the Stonehenge stones and Jinpei and the boys are taken away. Ryu is left behind. He meets up with Ken and the others. They want to save Jinpei, but can't approach because of a strong barrier in form of a dome. Elsewhere, Jinpei has heard the whole secret of the base. He tricks Gel Sadra, taking advantage of her way of thinking, and escapes the holding cell, taking the solarshifter's programming chip with him.

Big movements of the Earth's crust occur at the North Pole. Immediately thereafter, the adventurer Shimomura leaves Greenland on his way to the North Pole. He is reported missing on the third day of his voyage. By coincidence, he discovered a Galactor base and has been shot. When Ken learns that his teacher from school, Shimomura, is missing, he goes on a search mission to the North Pole together with the other members of the Science Ninja Team. However the God Phoenix cannot go all the way to the pole because of the influence of the magnetic field. During the search, Makku, Shimomura's beloved dog, has been discovered. He alone escaped the Galactor attack. Ken takes it with him and continues the search alone, not knowing that Shimomura is already dead. Makku leads Ken back to where Shimomura was shot. There, Ken also discovers the Galactor base. He tries to contact his teammates, but due to the magnetic field, he cannot get a connection.

Galactor releases test waves of the solarshifter. At the same time, in the city of Owari, accidents due to anomalities in the main computer keep happening, which provoke a panic. The Science Ninja Team goes to Owari in order to find out the reason for all this. But when they arrive in the city, Pimer and the New God Phoenix also cease to function properly. Galactor takes advantage of this opportunity and attacks with hang gliders. In order to return their attack, the Science Ninja Team leaves the God Phoenix, but Joe's condition is not good. Ryu returns to G-Town with the God Phoenix. Joe is not to be deterred though and starts his attack. However, the huge shield of electromagnetic waves around the solarshifter affect his cyborg body in a bad way. He gets into a critical situation and becomes unconscious. He is saved and treated by Dr. Raphael, who revives him. Even though Dr. Raphael warns Joe about the electromagnetic field, Joe does not want to let down his friends.

A spaceship from Earth is suddenly attacked by meteorites, and the Science Ninja Team hurries to the bottom of the sea, to the spot where the meteorites fell. But there, mysterious robots that arrived a bit earlier, are already collecting the meteorites. Is it Galactor...?? Joe follows the robots and corners them, but they are not Galactor. On the contrary, they greet him as "brother". They are cyborgs as well who have been made by Dr. Raphael. A cyborg who introduces himself as Ulf leads him to their colony. There he meets Ulf's comrades, who are equally friendly, as well as Dr. Raphael. Then he learns that they want to invite him to a strength experiment. Before Joe's eyes, many cyborgs die when they are tested under extremely hard conditions. Then Joe is called by Ken and has to return to G-Town. Elsewhere, Galactor has noticed the existence of Ulf and the others. Using the meteorite's guidance system, they let meteorites fall onto the colony and destroy it.