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A cikin 2065, Duniya tana tsakiyar yaƙin tare da ƙarin baƙi masu girma waɗanda ake kira Nova. Theungiyoyin sojoji sun haɓaka kuma suna horar da Pandoras, daughtersa daughtersa mata waɗanda zasu iya amfani da ƙwayoyin halitta na musamman da ake kira Stigmata (Seikon) Don nuna tsarin yaƙi da ƙwarewa fiye da ɗan adam. Tallafawa Pandoras abokan tarayya ne maza da ake kira Limiters, waɗanda ke amfani da iko na musamman "daskarewa" don taƙaita theirancin gasar su.

Duk wani daga cikin waɗannan masu iyakance shine Kazuya Aoi, wanda latear uwanta marigayiya 'yar Pandora ce. Kazuya ta haɗu da Pandora mai ƙarfi, Satellizer el Bridget, wanda ake yi wa laƙabi da Sarauniya Taɓaɓɓu, a kan salon kiranta da kuma matsanancin ƙyamarta yayin halartar Makarantar Koyon Ilimin Halittar Yammacin Japan. Duk da gargadin da abokan makarantar sa suka yi na kauracewa Satellizer, Kazuya ta yi abota da ita, kuma ta nemi zama Limitar ta. Satellizer ta yarda ta yi tarayya da shi, duk da cewa ba da daɗewa ba za ta faɗi a cikin gasa a cikin sha'anin soyayya mai suna Rana Linchen, wacce ta yi imanin cewa Kazuya abokiyar rayuwarta ce bayan ta tallafa mata ta fannoni da yawa da ta yi da abokan hamayyar kwaleji na sauya matsayi da kwasa-kwasai. Lokacin da Novas suka far wa kwalejin su ta amfani da Pandoras a ƙarƙashin ikon su don samun damar zuwa dakin binciken karkashin ƙasa na makarantar, an kawar da gasar su.

Satellizer da Kazuya sun haɗu da ofan Westan makarantar West Genetics zuwa dakin gwaje-gwaje a Alaska, inda zasu iya taimakawa tare da aikin Evolution Pandora (E Pandora), tare da bawa mata masu al'ada damar samun dashen Stigmata su zama Pandoras. Lokacin da ɗayan E Pandoras ya tashi tsaye, sauran za su bayar da shawarar ko magungunan da ke cikin gwajin ba masu haɗari ba ne, amma an yi su ne don yin biyayya ga fatawar ƙungiyar kasuwancin har da manajan. Bayan gano cewa har sai an kashe su, za a yi amfani da su, E-Pandora Amelia Evans ya jagoranci tayar da hankali wanda ya karu zuwa cikakke a kan Nova Clash.

Kazuya ya sami ƙarin bayani game da haɗin gidan danginsa da Nova da Pandora. Kakan Kazuya Gengo Aoi ya sami irin wannan aikin, wanda ya sanya Rana da Satellizer a cikin wata ƙungiya ta musamman tare da mata da ake kira Valkyries. Koyaya, a duk lokacin da aka gudanar da zanga-zangar tare da Nova da aka ƙera wanda yake ɗumammu, Pandoras yana da ilimin yaudara, haka kuma Nomy mai ruɓe ya zama tarin 100s na Nova waɗanda ke yanke Genetics. Gengo yayi la'akari da wannan ta hanyar sakin manyan Pandoras wadanda sune kawunan Kazuya. Cheoƙarin Chevalier don kashe Gengo yana amfani da masu laifi da yawa da ake kira Busters, lokacin da wasu kaɗan daga cikin Legendary Pandoras suka canza zuwa Novas mai kisa, amma aikin ya faɗi.