新城英治夜里醒来，竟发现自己相依为命的哥哥昭是一名武艺高强的剑客。若干年后，英治在哥哥的指引下成为了一名出色男子汉。 如今，“斗神大武会”重开，收到邀请函的英治和八位前所未见的强者一样，受到命运之绳的牵引，踏上旅程，一起齐聚在宿命的舞台——斗神大武会。

For one year, Master Swordsman Eiji Shinjo has been haunted by the memory of his battle with the renegade champion, Gaia - a battle that was cut short by the forces of the malevolent syndicate known as "the organization."

Denied victory, Eiji left the tournament followed by his opponents mocking laughter. Worse still, Eiji walked away no closer to finding his long lost brother, Sho. But now, a mysterious warrior is hunting down the champions of the previous tournament and using their own moves against them - and it looks like that person may be Sho. Who is this powerful new foe and who is his next target?

Eiji and Kayin, his closest friend and greatest rival, struggle to unravel the mystery before they, too, join the ranks of the defeated. The answer lies at the heart of the Organization and its plans for world domination. At last, the ultimate battle between the greatest fighters in the world will be decided. But if Eiji loses, his friends - Ellis - may Die...

ストーリーは第1作目と『2』を繋ぐオリジナルストーリー。Vol.1ではウラヌスに操られてエイジと戦うソフィアや、結社の作り出したショウと瓜二つの闘神兵との戦いが描かれ、Vol.2では結社の罠にかかったエリスを救うためにエイジ達ゲームのメインキャラクターが結社の本部へ乗り込むという展開となっている。