STAGE 01 in Nightshade (Kunoichi) takes place atop a Nakatomi fighter jet in the 23rd district of Tokyo. This is the same district where the Golden Palace popped up in Shinobi (2002). This district has been blocked off since the events of Shinobi and it is where the Golden Palace pops up again in Nightshade.
You encounter several different types of enemies in STAGE 01. The most common ones being Nakatomi's ninjas called Geni-Warriors. The Samurai and Shield Geni-Warriors specifically. Periodically the Nakatomi jet accompanying the one you are atop fires missiles at you that you must either dodge or kick back at the jet that fired them. The jet you are atop also deploys cannons that can detect your movements.
The boss for STAGE 01 is Kurohagane, Nakatomi's cyber-ninja.