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In the ensuing chaos, Psyga kidnaps Mari this causes dissension among the ranks of the resistance while Takumi races to Tokyo to rescue Mari. Using a special serum devised by Professor Nomura, Keitaro Kikuchi manages to change into Kaixa and save Mari from an Orphnoch, but the Kaixa belt quickly dissolves into dust as a side-effect. Meanwhile, Smart Brain stages another attack on Paradise. Yuka is gored to death and Naoya is eaten alive by the Elasmotherium Orphnoch while Smart Lady tricks Yuji into thinking Mari betrayed them. The next day, the three Orphnochs enter Smart Brain headquarters to fulfill their mission - only for Murakami to unleash the gargantuan Elasmotherium Orphnoch on them. Yuji kills Mizuhara in self-defense and recovers the Faiz belt before handing it back to Takumi, but the resistance exile Yuji, Naoya and Yuka from the group until they prove themselves they can steal the Emperor Belts. Shortly after giving Takumi back his Faiz Blaster, Mina is fatally shot by resistance member Mizuhara - who steals the Faiz Belt. Mina reveals to Takumi that years ago, her father found him badly wounded from the previous Riotrooper attack and implanted false memories in him. Furthermore, members of the human resistance suspect he is an Orphnoch himself due to his ability to become Faiz. Takumi, however, is not pleased that Mari had spread rumors of him being mankind's savior while he was away.
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That night, Takeshi and Mari meet at a masquerade ball, but when Riotroopers ambush the party, Takeshi regains his memories as Takumi and once again becomes Faiz - who is reunited with Auto Vajin while dispatching the attackers. Psyga attempts to take the Kaixa Belt, but he is warded off by the three Orphnochs allied with the humans. During the attack, Masato Kusaka/Kamen Rider Kaixa battles Psyga, but is quickly defeated and killed. When Yuji, Naoya and Yuka approach the human resistance and notify them of Psyga's power, Paradise is suddenly invaded by Riotroopers. Meanwhile, in a human refugee camp known as "Paradise", Takumi has been living a different life as a cobbler named Takeshi and shares a home with a girl named Mina. Murakami then discloses the existence of the Emperor Belts by introducing the Orphnoch Leo, who changes into the powerful Kamen Rider Psyga.
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The Orphnochs Yuji Kiba, Naoya Kaido and Yuka Osada wish to see both Orphnochs and humans co-exist in peace, but they are not taken kindly by the humans while Smart Brain chief Kyouji Murakami (who is now reduced to a head in a water tank) reminds them that humans no longer have a place on Earth.
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Since then, his friend Mari Sonoda has formed a human resistance group that have staged attacks on Smart Brain's headquarters in an attempt to steal the top-secret "Emperor Belts", but to no avail.
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Kamen Rider Faiz - was regarded as mankind's savior until he was presumed killed during an attack by Smart Brain's Riotroopers. Paradise Lost is considered as a continuation of an alternate ending, in which Smart Brain and the Orphnochs have won the war after the events of the Lost World, after Smart Brain used an experimental flower to turn humans into Orphnochs, Smart Brain has accomplished its goal of world domination - with 90% of Earth's population being Orphnochs while the human race is diminishing to near-extinction.
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