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In the 22nd Century, mankind has well overpopulated the Earth, and the outer planets are being considered for terraforming and colonization. The United Earth Federation approves of the Solar System Development Organization's "Jupiter Solarization Project," under the command of a brilliant young scientist, Dr. Eiji Honda. The project will "solarize" the planet Jupiter -- transforming it into a miniature "sun," thus providing life-giving warmth to the outer planets, making them habitable for human life. SSDO Chief Honda and his "JSP" team, take over Jupiter's Minerva Station, a giant orbital satellite which will serve as the JSP¹s nerve center for construction of equipment needed.
Meanwhile, across the solar system, while blasting a glacier to provide dammed water on Mars, a terraforming team discovers huge symbols carved in the surface (under the cleared glacier), which resemble the ancient Nasca markings back on Earth. Dr. Millicent Wilem, a space linguist, is sent to Minerva Station with her readings of the strange marks. Meeting with Honda, Dr. Wilem shows the translations of the drawings to be the record of the eons-old passage of an alien fleet through our system, its orbit and trajectory over Jupiter, and the loss there of one of their vessels due to the planet¹s gravitational pull. Dr. Wilem concludes that this must be the explanation for the old space explorers¹ mythological "Jupiter Ghost" story -- a sort of a cosmic "Flying Dutchman." Preparations are made to investigate further.
Due to the unusually low number of comets in the vicinity of Pluto's orbit, and with no response from two unmanned probes, Honda¹s old friend, space pilot Captain Kinn, is sent to investigate the phenomenon. He and astrophysicist Dr. Inoue are put in cryonics for the months-long voyage to Pluto aboard the exploration ship, "Space Arrow."
A radical faction of the "Jupiter Church" (a politically moderate, separatist organization of naturalists, which resides on a South Seas island and rejects technology), causes havoc on Minerva in an attempt to stop the JSP Project; they fail. While detaining the vandals, Dr. Honda discovers his childhood love, Maria Basehart, among them, and takes her to his cabin for a lover's reunion -- he wants her to leave her organization, and she wants him to give up the JSP Project and live with her back on Earth. Emotionally torn, Maria is sent back to the Jupiter Church with her fellows.
Drs. Honda and Wilem descend into Jupiter's ionosphere in an atmospheric vehicle, to probe the "giant red storm" -- the suspected area in which the Jupiter Ghost might be laying. Just as they receive the first aural and visual contact with the stranded alien vessel (sending out an SOS signal which is similar to whale cries), their ship is damaged, and the mission canceled.
As the Space Arrow nears the Pluto area, suddenly the ship is violently cast about by an outside force, and before the two men can awake from their artificial sleep, the Space Arrow is literally pulled apart, causing the ship to disintegrate. When the force subsides, space is still once again.
Dr. Mohammed Mansur, on Moonbase, leads the investigation on the Space Arrow disaster. Via extensive computer analysis and cross checking, he comes to the horrible conclusion that a rogue black hole is entering our solar system on a direct course for the sun.
Mass emigration to Barnard¹s Star, an impractically enormous project, is still considered by congress, as the "EX Project," until Eiji Honda forces his way into a closed meeting and proposes to alter the JSP Project, by throwing the solarizing Jupiter into the path of the black hole, to either change its course or destroy it. SSDO Chairman Webb disapproves strongly, but, the United Earth Federation President, seeing no other hope, approves the plan. Ignorant of the entire impending disaster, the unknowing public is to be told nothing. As a back-up to the new "JNS Project," construction of emigration ships begins, in case of failure.
With "B-Time" (zero hour) nearing, Minerva is reduced to a bare skeleton crew of SSDO techs and security personnel, while Dr. Honda makes preperations at Lunar Mission Control. After Dr. Booker, acting as a proxy to young computer genius, Carlos Arnez, is killed when his shuttle mysteriously explodes, Dr. Honda suspects the Jupiter Church, and goes to Earth to directly confront the organization. Honda only finds a peaceful commune, its members unable to concieve of murder. Upon returning to Minerva, Dr. Honda orders all personnel to begin evacuation, apart from himself and two security officers -- leaving the station at the final hour.
Anita, leader of the radical Jupiter Church faction, doesn't see eye to eye with the church's founder, a peaceful ex-pop singer named Peter. Finding his attitude too passive, she bands together her faction, drugs them with a fear suppressant, and leads them on a suicide mission to Minerva. Completely unaware of the bigger picture at hand, they plan to cripple Minerva's main computer in order to halt the solarization process. With forged documentation, the suicide team makes its way to the Jupiter outpost unnoticed.
Spoiler ! the end of the story is revealed below…
A flux in programming forces Carlos to stay in order to stabilize the systems in the Central Regulator. As he works, the radicals plant their timed explosives. Caught red-handed by security, a battle ensues, killing all but Carlos, Honda, and one last saboteur. Honda sets Carlos off to the last evac ship, "Flashbird 7." Computer-scanning for saboteurs, Honda discovers the location of the bombs and the remaining radical. After mortally wounding the saboteur, he discovers it is Maria. Rounding up all the explosives, Honda ejects them from the station -- except one. Badly injured, Honda joins his love in one last embrace as solarization begins. As the last "cries" of the Jupiter Ghost are heard, Minerva Station slips into the vortex.
At Lunar Mission Control, the staff watches in silence as the solarized Jupiter jumps out of its orbit and knocks the rogue black hole out of the solar system. The menace was gone, but so was a great man. But the human race could wake up and live again.