In the year 1614, Two ninja clans, Tsubagakure of the Iga and Manjidani of Kouga, battle each other to determine which grandson of Tokugawa Ieyasu will become the next shogun, in a competition that unleashes a centuries-old hatred, testing the love between the two young leaders, Gennosuke and Oboro, who are forced to choose between their duty to their clans or their love for each other.

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Some TV shows that have similar genres and were produced around the same time as Basilisk include Mobile Suit Gundam Wing, Spriggan, Mobile Suit Gundam: Iron-Blooded Orphans, Mobile Suit Gundam: The 08th MS Team, The Legend of the Galactic Heroes: Die Neue These, Samurai Warriors.