Takeru Myojin is visited by the evil Emperor Zule of Planet Gishin, who claims to be his father in his dreams. In his dream, Emperor Zule reveals Takeru was sent to Earth to destroy it, but Takeru rejects his orders and brushes it off as just a dream.
To find out the truth, Takeru visits his parents' home. There, his father, Professor Myojin reveals Takeru is not his biological son. Suddenly, his parents' home comes under attack by another assassin from Planet Gishin, who possesses Esper powers.
After analyzing Gaia's command capsule, Commissioner Otsuka discovers its secret. While the other Crasher Squad members leave for battle, Takeru is ordered to stay behind and is kept in confinement.
The other Crasher Squad members are suspicious of Takeru, due to his Esper power and mysterious ability to control Gaia. Now, Takeru must face the Gishin assassin alone.
After hearing his fellow Crasher Squad members say they cannot fight alongside a Gishinian, Takeru takes off into space with Gaia. However, using Takeru's absence on Earth as an opportunity to strike, the enemy attacks Earth.
The Gishinians finally discover where the Six God robots are stationed. They attack Egypt where Sphinx, the body unit of God Mars, is located. The Crasher Squad is sent as reinforcement and a battle ensues.
A giant space fleet has left Earth to construct a base on Pluto and the Crasher Squad has been assigned to guard the fleet. However, Takeru hears a mysterious voice in his head urging him not to go to Pluto.
Takeru bombs the Spaceport and a young boy, who admires Takeru, witnesses him in the act. With pictures to prove his guilt, Takeru is taken into custody. With Takeru out of the way, the Gishinians' ships approach Earth.
A massive earthquake triggers Tokyo to slowly sink. However, the earthquakes do not seem like a natural occurring earthquake. What is causing the earthquakes and can Takeru stop Tokyo from sinking beneath the sea?
Takeru and Namida head to the Space Control Center to secretly investigate the cause of the frequent collisions between spaceships. The Director of the Space Control Center and his granddaughter welcome them, but Takeru discovers his granddaughter is actually a Gishinian. Will Takeru be able to expose her secret and discover the cause of the spaceship collisions?
A mysterious voice alerts Takeru that the Gishinians are plotting to assassinate the President. However, it was a trap laid out by Sagule, the Gishinian Spy Commander, in order to find out who is behind the mysterious voice.
Marg is finally captured for treason and is ordered to kill Takeru in exchange for his life. Meanwhile, back at Battle Camp, Takeru receives a transmission from the mysterious voice, wishing to see him on Saturn.
Marg is recaptured and taken back to Planet Gishin. A devastated Takeru chases after his brother, but the evil Emperor Zule appears and stands in his way. Faced with Emperor Zule's invincible power, will Takeru be able to defeat Zule and get back Marg?
Marg, whose memory has been erased by Emperor Zule, becomes a Gishinian Commander. His mission is to kill Takeru, the traitor. Meanwhile, back at Battle Camp on Earth, the Gishinian spies have taken Shizuko and Namida hostage.
Marg, who has been stationed at the front-line as a Gishinian Commander, launches a series of attacks on Earth's major cities. Takeru fights the Gishinians with all this might.
The moon base is under attack and the Crasher Squad is dispatched as reinforcement. Meanwhile, Loze, Marg's Lieutenant, infiltrates the moon base and takes over Mika's body. Loze begins sabotaging the base from the inside, but is found out by Takeru.
Takeru and Mika are shocked when they learn Akira has a new girlfriend. On his girlfriend's request, Akira shows Akane around the base, but it's all a trap. Once inside, Akane begins planting bombs throughout the base.
Takeru visits a secret base on the South Pole that's researching the Warp Catapult. However, his visit is cut short when he learns that Battle Camp under attack by Marg.
Takeru and Marg are locked in a fierce and decisive battle. During the battle, Marg regains his memories and their hearts connect once again. However, their reunion is short lived, as fate separates Takeru and Marg once again, this time forever.
In order to avenge Marg, Loze takes Commissioner Otsuka and Shizuko hostage and challenges Takeru to a duel. To secure his mother and the Commissioner's safety, Takeru accepts Loze's challenge.
Touched by Takeru's kindness, Loze begins to doubt her reasons for serving Emperor Zule. A conflicted Loze visits her home planet and is inadvertently captured by a guerrilla squad that is fighting the Gishinians.
The Crasher Squad heads to Planet Gishin to negotiate a peace treaty with Emperor Zule. However, the Crasher Squad becomes engaged in a fierce battle against the Gishinian fighter squad.
The Crasher Squad is caught in a space storm and makes an emergency landing on a planet disguised as Planet Gishin. Emperor Zule suddenly appears before the Crasher Squad and attacks them.
The Crasher Squad finally lands on Planet Gishin. However, the evil Emperor Zule is determined to defeat Takeru, even if it means destroying Planet Gishin along with him.
A month has past since the battle on Planet Gishin. The Crasher Squad, who has been newly assigned to Ceres Space Station, rescues a girl named Flore out in space.
Flore, a negative Esper, shows nothing but intense animosity against Takeru, who is a positive Esper. Then, a ship from Planet Marmelo appears and demands they hand over Flore.
A mysterious pirate ship suddenly appears near the space station, as though they were guided by Flore's telepathy. Gash, the pirate gang leader and his men infiltrate the space station.
Takeru learns Flore is sending her telepathic messages to her fellow negative Espers, who escaped from Planet Marmelo before her. Gash, the pirate leader, appears with his pirate ship and claims Flore is their fellow comrade.
Flore leaves Ceres Space Station to determine if the people on-board the pirate ship are truly her comrades. She confirms Gash and his pirates are fellow negative Espers, but she can't bring herself to join a ruthless band of pirates.
Flore finally opens up to the Crasher Squad and reveals the tragic fate of the negative Espers born on Planet Marmelo. Then, Ceres Space Station receives a transmission from Planet Marmelo.
Planet Marmelo declares war on Earth. Takeru and Flore are held responsible for the outbreak of war and are imprisoned. Meanwhile, the Marmelonian Forces begin an all out attack on Earth.
Gash tells a captive Flore the wretched life the negative Espers were subjected to by the positive Espers. Meanwhile, Takeru heads to space alone to rescue Flore. Led by Flore's presence, Takeru and Gash come face to face on an asteroid belt.
The Cosmo Crasher is under attack by the Marmelonian Forces and Takeru is determined to save his friends. However, Takeru who is hit by the Brainwave Disrupter Rays is unable to combine the Six God robots.
The Earth Forces launch an attack on Gash's pirate ship to take back Flore in hopes of handing her over to Planet Marmelo and thus ending the war. However, the Earth Forces are defeated and Takeru is taken captive during the battle.
Flore heads to Planet Marmelo to find out if Gyron, the ruler of Planet Marmelo, is her father. However, she becomes lost in a dark nebula, known as the space cemetery. Takeru dives into the space cemetery to save Flore.
Takeru and Flore head to the palace to see Gyron in order to convince him to stop the persecution of negative Espers and to stop the needless attacks on Earth. With Armo, Flore's mother and Shikeel, the spiritual leader of Planet Marmelo taken as hostage, Flore and Takeru surrender themselves and are crucified to a cross. Will Takeru and Flore escape certain death?
Upon his return to Earth, Takeru is suddenly dismissed from the Earth Defense Force. In despair, Takeru disappears along with God Mars. Shortly after, the Galilei Base is destroyed by God Mars.
Takeru tries to return to Earth, but is stopped by the Crasher Squad. The Earth Defense Forces were still under the impression that Takeru had destroyed the Galilei Base.
Takeru joins the Crasher Squad once again after Naoto proved his innocence. Meanwhile, Gash and his pirate ship fleet leaves for Planet Marmelo, but come under attack by the Marmelonian Forces, which outnumber and outgun his ships.
Gash is determined to defeat Gyron, the ruler of Planet Marmelo and refuses the Crasher Squad's help. Meanwhile, Gyron captures Shikeel, the spiritual leader of Planet Marmelo, who sides with the rebels, and prepares his execution to lure out Gash.
Gash is determined to defeat Gyron, the ruler of Planet Marmelo and refuses the Crasher Squad's help. Meanwhile, Gyron captures Shikeel, the spiritual leader of Planet Marmelo, who sides with the rebels, and prepares his execution to lure out Gash.
Gash infiltrates the enemy base alone to save Mika, an uncharacteristic move for a man who is known for his ruthlessness. After rescuing Mika, the two escape on a snowmobile, but the enemy stands in their way.
Gyron orders the deployment of the powerful Magnetic Cannon to destroy God Mars. Kiel, the inventor of the Magnetic Cannon, adamantly opposes its use, as it will greatly alter Planet Marmelo's geomagnetic field.
Realizing God Mars will come undone, Takeru decides to attack the enemy base with the Six Robots separately. The Marmelonian Forces use the Magnetic Cannon to defeat Takeru once more, but are unable to keep up with Gaia's speed.
Flore rushes to the palace to put an end to the battle against Gyron. Knowing Planet Marmelo is on the brink of destruction, Gyron flees the palace while dodging Flore and Takeru's attacks, and evacuates to space. Flore and the other survivors must escape to the sea. Suddenly, the Planet of Death appears in the Marmelonian sky. Will Flore and her people perish along with Planet Marmelo?
Planet Marmelo's destruction is now only a matter of time. When all hope seemed lost, its twin planet, the Planet of Death, had suddenly transformed into a habitable planet before their very eyes.
Gyron's forces have entered the solar system and are quickly approaching Saturn. Kenji, who has been newly assigned as the Commander of the Earth Defense Force, battles against the enemy forces.
The Earth Defense Forces are engaged in a battle against Gyron's forces from invading Earth. Takeru and the Crasher Squad fight bravely, but the enemy succeeds in destroying Ceres Space Station.