In this game, a follow-up to the original Shinobi, once again you are Joe Musashi, but this time you're not out to free hostages, but to gain your revenge on the 'Neo Zeed' bandits. The story told is that the old enemies 'Zeed' from the first Shinobi game has reorganised, and they have now struck back at your clan, first by killing your old master, and then kidnapping your bride. What you have to do is go around killing enemies with "kunai", or throwing knives, and find the exits on each level. You can also find power pack upgrades by breaking boxes - though some are booby-trapped with bombs. Once you touch an upgrade, your knives turn into fire and you have a ninja sword. Extra knives and health are also sometimes in these boxes. There are eight zones to pass through on the map, each having three levels, with a boss at the last level of each zone. Standard enemies vary from ordinary WW2 type soldiers, shooting rifles, machineguns and throwing stick grenades - to ninjas with shurikens throwing stars, katana swords and chigiriki-type flail weapons. Some types of enemies only appear in specific environments. The environments are kept in similar style within a zone, starting out in a traditional rural town and forest area with ninjas and attack dogs, next into a modern city with an airport and factories, defended mainly by soldiers, moving onto a highway with almost frogger-style jumping to avoid cars, soldiers and jumping enemies disguised in nun-outfits (nun-jas?), next into an entertainment districts on rooftops and backstreets with ballet-dancing enemies, escaping on a train (riding on top of course, a shinobi won't buy tickets) to a harbour with more soldiers and cannon towers, and ultimately to the island where the final boss of the Neo Zeed bandit resides. The zone bosses varied with each release, as there were licensing issues preventing their free use - initially several well known cinematic characters were used: Godzilla, Batman, Terminator and Spiderman, but they were gradually replaced with other characters, sometimes varied only by simple palette changes.

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