A year after the events of the Grand Celesta Galaxy, a young Italian entrepreneur named Vicenzo Mainetti, known for coaching numerous young players from all over the world reaching the calibre of Mark Evans, announces a new world youth tournament named Football Frontier Third Imperium.

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In this new tournament, not only Special Moves, Fighting Spirits, and Armourfied Fighting Spirits are allowed, but young people between the ages of 13 and 19 can participate without distinction between age groups.

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However, it is feared that the tournament itself could be ruined by Laphya, a new drug used by young people to increase their hidden abilities and improve their physical strength, and is also undetectable with a normal doping test. Therefore, to prevent any sort of accident, some specialised players will be personally chosen by Vincenzo to identify the Laphya users, including the young Specialist Shō Ishida, who, unlike his other peers, will try to find out what there is really behind Laphya, and the much coveted award of the FF3I, which seems to be somehow connected to his clouded past.