There's another door here - take that to reach the Middle Cabin. Break down all the wooden boxes here (but make sure to avoid the crates) and then look for a small crank you can turn. After turning it a bit, you'll be attacked by another wave of troops - but you know how to handle these guys by now, right? Right. Once you've handled that problem, return to the crank and resume the turning.
Now, you'll need to catch onto a line running across to the platform you see in the distance. Unfortunately, there are also soldiers on said platform that will attempt to shoot you as you're making your way over there. Take them out with a few arrow shots, then cross on over. (If you happen to run out of arrows, there's a box in the Middle Cabin that will give you a free refill.) There's another guardian waiting here for you - it goes without saying that you'll need to dispose of him. Grab the nearby treasure chest, then use your weapon to smash the very conspicuous broken window nearby. Jump through the broken window and make with the choppity to cut up the system's wiring and disable all the locks in the ship. Now you can finally reach the boss!
Backtrack all the way to where you first began (also, save your game) and enter the previously locked chamber that was near Hayabusa's room. Make sure you're ready first...
One of Ninja Gaiden's most notorious challenges is the sixty-enemy challenge rooms scattered throughout the game. In these areas, enemies will appear, 3 or 4 at a time and will constantly respawn until you chop down all 60 of them. When you finish cleaning up, you'll receive a rare and valuable item for your trouble. This is the first such room in Ninja Gaiden Sigma and it's a tough one. You'll be fighting mostly white-suits with a few black defenders at first, but after you clear out a bunch of them, blue-suited troopers with napalm guns will start to join the fray. Obviously, getting hit with their projectiles will not be very beneficial to your health, so switch your focus to them once they start appearing, then go back and take on the remaining foot soldiers. A good technique to use is the Izuna Drop - not only does it pretty much kill the poor sap caught in it, it also sends out a small shockwave that damages other enemies in the immediate vicinity, which is great in a situation like this. While the soldiers frequently drop blue essence after being offed, you'll most likely still need a few health refills, so don't hesitate to use some Elixirs if need be. The reward for your patience and persistence is a Lives of the Thousand Gods (along with all the yellow essence you've collected over the course of the fight). That's not the only treasure here, though - climb the mountain of crates using your ninja jumping skills to discover another Golden Scarab.
Now, head on back to the Main Cabin and through the double-doors you unlocked previously. At the end of this hallway, you'll find another door that was once locked. Not anymore! Since the control system is down, you are free to pop on in. You'll wind up in an area with a few soldiers and a lot of ledges. You'll need to do some jumping here, as well as some enemy elimination, of course. There's one hidden item to look out for here: find a metal crate on the walkway above the metal stairs. Jump on the side of the crate, then flip off backwards to reach a higher platform with another Golden Scarab.
At the end of this room is a long ladder. If you try to ascend, you'll be given a message telling you the hatch is locked. However, you'll notice there is an opening to the side of the passage leading up. From the bottom of the ladder, use your wall flip technique to ricochet off the walls, springing upwards until you reach this small cul-de-sac. Flip the switch here to open up the hatch. Save your game and then climb up the ladder to fight...
Stage 3 Boss: Dynamo
Ugly has a name and it is called Dynamo. This sack of lard is packing enough heat to make for a pain of a boss, unfortunately. At long range, he'll fire rapid energy shots at Ryu. These can be avoided by simply running perpendicular to Dynamo. At medium range, he creates a damaging electrosphere around him. And at close range, he has several hard strikes and grab attacks. He can be tough to approach and once you do get near him, you have to worry about getting grabbed and pounded. What to do? Well, dashing and jump attacks are a good option - they'll chop clean through him and put you at a decent distance away from him. Even if it's not far enough to dodge anything he'll counter with outright, it still allows time to get away from him. As always, perseverance (and maybe some healing items) is the ultimate key to taking him down.
Now, it's time for Hayabusa to begin his vacation in Dworku. Unfortunately, they don't take too kindly to tourists here, as we're about to find out.