The final round still takes place in the docks, but it is now night time. Along with many soldiers, these docks are also guarded by cannons, which will shoot fireballs. The cannons can also move up and down to try and lock on to where Joe is, and cannot be destroyed. They can, however, be used as platforms by jumping on the top of them. As in the previous round, one of the main hazards here is the risk of being knocked into the water by enemy shots and grenades. Try shuriken spraying everything if needed.
Other enemies include the nunchaku users, but for the most part the soldiers are the real threats in this section. Time your jumps carefully and don't try and rush through this part. Near the exit there is a health item to collect.
The second section of the round is what most people consider to be the most difficult and frustrating part of the game. Joe is in a huge maze, where there are several doors and floors to move around. There is a correct path to get to the boss, but finding this path is a case of trial and error. Doors with handles on them are doors you can move through -they will automatically open when you stand in front of them, and take you to another place in the maze.
The maze is full of enemies, with nearly every one encountered in the game so far showing up at some point. There are a few hidden surprises that can help, in secret areas in some of the walls (try ducking through a black part of one of the walls). As this maze is so difficult, I would recommend watching this video to see the correct route, or checking out this map created by Nash.
You'll know you are on the right track if you come across a room full of gray ninjas -head through the door in the bottom left corner. This will take you through a door you cannot go back through, and there is only one way to go: towards the exit.
The final enemy of Revenge of Shinobi is The Boss, who is the leader of the Neo Zeed. In the background Naoko is trapped in a cell. When the boss appears, he will keep spinning his head around, using his hair as a weapon. You need to get in as close as possible.
When you do this, the boss will attack, but if you crouch, his strike will miss. He is vunerable when this happens, so quickly get him with a close-range attack and then move back. The boss will throw out his hair at you, and you'll need to jump to avoid it. Surprinsly that is it -this final boss isn't very difficult to beat at all.
One thing you do have to watch out for is Naoko, as she is in danger of being crushed. You can delay the stone slab by hitting part of the walls on the left or right. You'll need to defeat the boss as quickly as possible to save Naoko in time. If you manage it, the stone slab will move back up, whilst the boss will die an explosive death.