1. Murai  - Stay away from this guy as he'll make short work out of you with his grapples and combos. Instead Wall Run and perform and Head Splitter (Jump + Strong Attack). If you connect he'll be stunned for a short combo and run away and repeat. This fight is over once you get his bar over halfway gone.
2. Subboss - Samurai Fiends on Horseback - This was VERY annoying to me. You have to fight 4 of these enemies: 2 archers and 2 spear weilding samurai in sets of 2, one of each type.  First of all, you can use the bow to take these guys out but I found that method to be life consuming. Instead, when the samurai on horseback pass by and his horse reels up, hit him with a Head Splitter or quick combo and back off. It's gonna take a while to wear them down but it's easier to attempt this than shooting the bow in first person mode when you're a sitting duck to all of their attacks. Just have patience and make sure to return to Muramasa's shop afterward to replensish on supplies if you're dry on items after this fight.
3. Horselord - This clown is easy. Kill all his henchmen and stay away from him and shoot your arrows from a distance. If you hit him in the back of the horse it does double damage.
4. Machine Head - If you upgraded the Dragon Sword to Level 2 then use Flying Swallow (direction stick towards enemy, Jump + Strong Attack) just keep doing it until he's dead. If not use Head Splitters and roll out of the way at the last second (using Reverse Wind technique, hold Block button and move left or right) to dodge his laser blasts. You can try combos too but don't be greedy or he'll grab you and blast you through your chest, doing massive damage. Just make sure you never stop moving.
5. Troublesome Enemy - Exploding Shuriken Tossing Ninjas - Ok these guys are very cheap. Plus you always fight them in packs of 3 or more. Yeah, I've fought 5 at once myself and barely walked out alive. Make sure you take full advantage of the Counterattack (hit Weak or Strong Attack while blocking after first attack from enemy connects; only if you have the Counter Attack scroll) and the Flying Swallow attack. Make sure you take advantage of them lying on the ground too!! Do a ground attack and finish them off. If you manage to get a shuriken on you, do a Flying Swallow, Head Splitter, or Ninpo magic right before it explodes to avoid taking damage.
6. Subboss - Raptor Fiends - I suggest you be like a coward and use the hit and run method. Hit them with either a Flying Swallow or a Head Splitter and run and repeat until all 3 are dead. Watch out for their tail whip and bite attacks are highly devastating.
7. Fiend Behemoth - This is easy. By now you should have the Dragon Sword at lvl 2 or you wouldn't have gotten to the end of this stage. Just stay close to him and do Flying Swallow on his tentacles and his main body until he's dead. By the way, you'll run into this clown again in the next level and at other points in the game so use the same method.
8. Sub-boss - Undead in Ritual room - This isn't a boss fight but just as hard as one. Before you go into the room with the Chalice make SURE you got the Dragon Sword at Level 3 and picked up those Vigooran Flails. The easiest method to take them all out is to kill the archers first and then their axe-weilding friends. If they manage to jump on top of you and try to bite you, hold Block as it takes you down and mash the attack buttons. You should kick him off you before he even gets a bite out of you. You can use Flying Swallow to cut their heads off to disable that attack. Then you can use the Vigooran Flails to finish them off with the quick combos that can take out even two or three Undead at once. If you get backed up into a corner don't be afraid to use Ninpo magic.
9. Skeletal Dragon Fiend - This is pathetic in my opinion. Just keep doing Flying Swallow on his limbs and just watch out for his bones that he throws and the tailwhip. When he rams his head towards the screen, MOVE out of the way! This is the only attack he has that does major damage, but he rarely does it. I beat him on my first try and he didn't pull this off till I played the level again for fun on a retry.
10. Alma, Greater Fiend - Make sure the Dragon Sword is at Level 3 before taking her on. This chick is hard. VERY hard. With that said, I'll tell you straight out you'll prolly lose to her the first couple of tries in mere seconds. Don't get close to her (this makes her do her devastating grapple attacks or stomps) nor stay to far away from her (hurls stone pillars and energy blasts); stay somewhere in between. But still she'll nosedive towards you to try to hit you. You can jump over her easily and counter with a Flying Swallow after she flies under you. Then she'll fall to the ground, run in for a quick 5-7 combo and run. She usually gets up with her grapple move (light  shines around and below her, RUN AWAY from this!!). Repeat until she's defeated. I don't suggest using Ninpo magic either unless you know you can't dodge one of her attacks and need that split second of invulnerability.
11. Troublesome Enemy -  Armed Military Soldiers - I personally hate these guys. I personally suggest don't even try the Dragon Sword or Rachel's War Hammer. Those two weapons are TOO slow to take these guys down. I suggest the Vigooran Flails; these will be able to take on a swarm of these guys plus deal enough damage with their powerful combos to take them out with the ease amount of trouble as long as you keep the pressure on. It would especially help if you have this weapon upgraded to Level 2 for you can unlock the combo "Cremator" ( X, X, X, Right, X, X, X, X, X; as long as you can keep this one going. I've done it up to 106 hits, I've heard it can go on to 250 max.) In my opinion, the rocket launcher packing guys should be your first priorty to kill ALWAYS. You can shoot their rocket out of the air with your arrows but 9 times out of 10 you will be fighting these guys in close quarters combat.
12. Two Tanks - This fight is cheap in my opinion as the main flaw of this game is exploited in a boss fight: Ryu can't move while using the bow. Make sure your maxed out on Explosive Arrows and APFSDS Cores. Use Explosive Arrows to take out the gunner then while the tank is circling you without a driver, quickly shoot it in the rear for massive damage and destroy the tank. If you take too long, another gunner will appear. After you destroy the first tank, ANOTHER one comes to try its luck. Same method as before here too. Here's an alternate method I've found to beat these tanks without losing too much life: Ok, when the fight starts fire 2 arrows at the tank and kill the gunner. Then switch to Ninpo magic and use all the spells you got (at this point of the game you should have at least 3 flames for magic). This should destroy the tank for you, and look you haven't taken a scratch. When the other one comes, refill on Great Devil Elixir, take out the gunner, and repeat as before. I did this myself and made it out of this fight without using not one Elixir to heal myself.
13. Helicopter - Before you even get to the copter, here's a tip to kill those two rocket launcher packing goons with ease. As SOON as you see them fire their rockets, use Ninpo magic for a split second of invulnerability and kill them at the same time. See easy as cake. Now for the boss. When the helicopter flies in background take aim with your APFSDS Cores and get as many hits as possible before he comes into range for his machinegun and rockets. I've managed to knock off half of his lifebar before he got close. Don't worry this will take a couple of tries. When it gets close only fire your Core arrows at it when it's below the bridge you're standing on. When it fires it's missiles, run and jump to dodge them because you won't be able to shoot them all down with your arrows. If you run out of Cores, there's more at each end of the bridge you're standing on in a crate. Repeat til that copter is junk.
14. Communications Tower - This is easy once you figure out what your targets are. It's not the soldiers but the spotlights around them. Watch out for the soldiers though, because they're packing rocket launchers. If you see one coming your way, jump out of the way or shoot it down with your arrows. Knock out all the spotlights with your Explosive Arrows and this is a wrap.
15. Electric Worm - This is kinda hard but once you get the pattern you'll get it. Use the Windmill Shuriken to hit him while he's far away and use either the Dragon Sword or Vigooran Flails (if you're good you can score 20 hits on him before he reels back) to hit him after his body whip. After getting your hits make sure you're out of the middle of the platform you're standing on because the worm will spring out of his tunnel and bite you and toss you around, doing major damage. Don't jump in the water either as the worm will electrify the water from time to time, especially if you attempt a Flying Swallow.
16. 2 Electric Worms - This is just cheap in my opinion. This fight REALLY pissed me off the first couple times I did it. It's the same method as before but try to focus on one worm for you can be one on one with the final one as it seems to get faster when they are about to die. Forget the Flails, the Dragon Sword seems to be better suited in this fight.
17. Dragon Fiend - This guy takes a LOT of patience and a couple of retries. Before the fight make sure you are maxed out on ALL of your projectile weapons. Don't get close to him as melee weapons are almost nothing to him. Dodge those lasers he fires at your way. The lasers' trail will turn into flames and toast anything standing on them. When he flies up and takes a seat on one of the platforms above, get under him unless he begins to flap his wings; in this case, run away from him to avoid taking damage from his gust attack. Stay far away as possible and fire your arrows at his long head. This is his weak point. You're definitely gonna run out of arrows in this fight and don't be afraid to use Incendiary Shurikens either.
18. Doku, Lord of Greater Fiends - This is a disappointment that this guy isn't as hard as he seemed when Ryu and Rachel fought him. First of all, don't be stupid like Rachel and use the War Hammer. If you do, you'll end up like her over there in that cell. Instead, simply keep on hitting this guy with Flying Swallows. It won't connect at every strike but keep doing it anyway. Keep moving to avoid his attacks, with his charge up attack being his most deadliest. I beat this guy on my first attempt without using not one Elixir.
19. Abnomible Snow Fiend - Okay this will sound odd, suggesting a weapon other than the Dragon Sword but I found that the Vigooran Flails do WAY more damage to this guy than the Dragon Sword does. Plus Ryu seems to dodge faster with those during this fight. When the fight starts, the boss just stands there and lets you get in a few hits. I suggest you walk up to him and start off the fight with a Flying Shallow as to hit the buttons to go into a combo when you touch the ground and get a good 10-15 hits off him and about 1/4 of his life bar down. This is a simple boss fight and simple dodging is required. When he flips behind you, keep hitting the attack buttons the Flails follow the target automatically and will hit people behind you as well (this is usual to know for dealing with those clawed Fiends in the sewers). His two most devastating attacks are his ice blast and the bearhug but these are highly obvious to see coming. Jump to dodge these attacks, then run up to his side or his rear and get in a combo just like how you did when this fight started. As for normal attacks, when he pounds his fists on the ground in a fit, icicles come up from the floor. Run and jump to avoid this. Another attack is his one-two punch where he lunges forward with one punch and comes back with another hook from the opposite side. Jump away from the first punch and away from the next incoming fist and counter from the side of him with a quick combo.
20. Flame Worm - This is just as annoying as the Electric Worm fight. Keep the Dragon Sword out as that's the only weapon besides the Windmill Shuriken you're gonna be able to hit him with. Throw the Windmill Shuriken while you dodge his attacks for some decent distance damage. To dodge his fire circle blasts it requires last second jumping away to avoid. With his body sweep, either back up to the back of the room (away from the lava but with your back to the wall of  the door you came in at) or Wall Run to avoid this. Afterward rush in quick and get in a quick 5 hit combo before he reels back. Then move to make sure you avoid his quick spring out of the hole to attempt to bite you. Be careful of this attack as it's far more powerful than the Electric Worm's bite and does just as much damage as the Snow Fiends bearhug. Repeat this method until he's defeated. 
21. Flame Dragon - This fight is really nerve-racking to me as I was on edge to not get hit by this boss' most devastasting attack. To survive, make SURE you have a LOT of Devil Elixir to restore magic as it will be your guardian angel in this fight and maxed on Explosive Arrows for distance damage. Use Inazuma (Lightning Ninpo) on the dragon when he uses his fire wave he creates when he flaps his wings. Jump at the last second to dodge those fireballs and at all costs dodge/move out of the way of his bite attack!! This attack itself is sometimes a one-hit kill and/or does over 75% of your health is wiped off from it. If you do get caught in this attack, hit those Block + Attack Buttons like a maniac for Ryu can lift the dragon's mouth open and get free. Don't try a Flying Swallow either as you'll end up in the lava. The best time to hit the dragon is when he sticks his head in front of the platform you're standing on. Run up to him get a good combo off. If prefer this one (with default controls): X, X, Y, Hold Y (as it should go into either a Head Splitter or a Spinning Slash at the end if done correctly for at least a nice chunk of his life). Shoot those Explosive Arrows from a distance if he has somehow lost track of you. When he roars, he'll send a couple of the platforms up into the air to platform close to his head when he stands up vertically. Don't do this unless you are absolutely sure you can risk it and get some good hits on his head with Explosive Arrows. 9 times out of 10 he counter attacks with the bite attack so be careful. When he's close to dying, he sometimes goes into a loop of repeatedly doing either the bite attack or the flamethrower at the platform you're standing on (run the opposite way this is coming from to avoid or just jump over it).
22. Troublesome Enemy -  3 Purple Undead Military Soldiers - These guys are a major pain to kill but highly worth the trouble in Stage 13 when you first encounter them as your reward is a Talisman of Rebirth if you manage to kill all 3. Take them on as if they are the Undead from a few stages back. Use the Flying Swallow to decapicate their heads and/or arms off but be careful as this doesn't stop their grab attack like their relatives. Watch out for their swing of their gunaxe too as it swings twice and sometimes three times and does enough damage to worry about. Core Arrows work wonders on them as it goes through their heavy armor but you'll unload at least half your supply or more on just one, so follow up with Ninpo magic (Art of the Inferno preferred with they are bundled up together). Don't linger with long combos either as they will overwhelm you. Just hit and run. Rinse and repeat until that shiny prize on the ground is yours for the taking. If you don't want it, you can just run away from this fight and skip it altogether.
23. Lesser Alma -  This is basically the same fight as before but she's grounded for most of the fight and uses her uncanny speed in the form of a charging slash combo. This attack can be easily seen coming and you can block all of it but be careful of the grab from her spider-like torso at the end. She adds this in when you either block too much or just wants to catch you off guard. You can jump towards her during the charge with a Spinning Slash (tap Jump + Weak Slash) and land on her rear with a combo. If you know you can't dodge her attacks (the energy projectiles from the first encounter,the charging combo, or the column throw which she RARELY does this time), simply use a Ninpo spell, preferably Art of the Inferno which should be at Level 3 at this point of the game. This will absolutely dissimate her from first of the flames that are around it at start if she's close then the blast afterward which should knock off at least 1/4 of her life off. Now since she's on the ground helpless from that, run up to her with a Flying Swallow and a combo to inflict even more pain on her. You can repeat this method if you want to beat her without wasting those 2 Talismans of Rebirth you should still have at this point of the game. Just have some Devil Elixirs handy. One thing to remember doing fight like the first time, as you should NEVER stop moving as Alma is lightning fast and her attacks will wear you down in no time if you're not on your toes.
24. Troublesome Enemy - Spirit Fish - Whip out those Vigooran Flails as those are the only weapons that can wipe these little pests away from you. Back that up with the Art of the Ice Storm Ninpo for even more protection. Be careful too as they can come in swarms and at least 10 or more of them can drain all of your health away. If they manage to knock you to the floor, hold Block and hit those attack buttons to get them off of you in a hurry as more will spawn if you stay on the ground too long. I had 20-30 on me once and that killed me instantly.
25. Troublesome Enemy - Laserblasting Fiend - These guys are cowards as everytime you encounter them they will have smaller henchmen backing them up, usually the Spirit Fish or Clawed Fiends.
26. Spirit Doku - This is a surprise that this guy isn't as a pushover as the last time...or is he? Well if you end up and try to fight him straight out as you try to block his fierce slashes, you'll be toast as he's so powerful that he breaks through Ryu's block after the first hit. You can use the same method as the first encounter with him (just pummel him with Flying Swallows) but make sure you're connecting with this before/after he attempts one of his sword combos. IF you can manage to hit him with a Level 3 Art of Inferno, he can say goodbye to a HUGE chuck of his lifebar. If you got those Devil Elixirs handy you can beat him with this alone.
27. Tentacle Fiend's Last Stand - Just the same pattern as before (stick close and use nothing but Flying Swallows) but definitely make sure to watch out for his tentacles this time though. He somehow got a brain now and tries to slap you out of the air before you attempt a Flying Swallow.
28. Return of the Snow Fiend - This is the same as before but in a smaller arena, but this works to your advantage as Wall Running on the walls of the circular arena makes it a whole lot easier to dodge his attacks. Stick with the True Dragon Sword too as it should end this fight quicker by Flying Swallows when his guard is down or after one of his attacks misses and add in a combo.
29. Arch Fiend - After being a coward by firing those fireballs at you while you were fighting his Clawed Fiend henchmen he finally notices you as a threat and takes you on. Oddly though this guy is pretty easy to say he's the one who commands all of the Fiends. When he summons his Clawed Fiend brotheren, use a Inazuma Ninpo magic to kill them all at once and damage the Arch Fiend. Sometimes he'll reel back and fall to the ground when you do this or any other time you hit him so take advantage of it with one of your best combos (look into your Combo List in the Options to find one you like), Dragon's Tail is really effective in my opinion. Watch out for his rapid fire fireball attack that he sometimes does to stop you from attacking him as he will sometimes cancel his current attack and go into this. Run and jump to dodge it. The best time to hit him with a Flying Swallow is when he's about to or after his shoulder charge attack. 9 times out of 10 the Flying Swallow will leave him open for a combo so do your thing.
30. Ultimate Alma - You're fighting her on a flying platform that you can move and jump off of and make a another appear to catch you. She's made up of 3 parts: right arm, left arm, and chest. I suggest you take out one of her arms first then the chest as it makes her beam attacks originate in front of it if its the last part to destroy. Dodge those beams too as they can be quite devastating to your health, especially after you destroy 2 out of 3 parts and they start to move faster. Remember if you can't dodge one of those beams simply use a Ninpo to get a split second of invulnerability and get a good deal of damage on Alma. If you can afford it, you can beat her with just Ninpo magic.
31. Dark Emperor - This guy's entire body is the target as you can damage all of the skulls but the one with the horns that's at the top or the front is the part that takes the most damage. Equip your Vigoorian Flails and Explosive Arrows and fire away at that skull. When the skulls glow, ready those flails and start breaking the skulls as they try to hit you. If you can't hit them all try using either Inazuma or Ice Storm Ninpo to protect yourself. For all costs, make SURE you dodge the last skull as the one with the horns will try to bite you, doing massive damage. After that attack he either walks around the arena with horned skull in front for easy picking from your Arrows or rarely tries to jump onto the platform you're standing on to crush you. Once you run out of Arrows don't be afraid to use your Incendiary Shurikens either as you can throw those faster than you can shoot arrows.
32. Dark Disciple - Finally, you get to fight the Kane wannabe. This has to be the easiest fight in the game unfortunately. Just as soon as the fight starts, run towards him and do a Flying Swallow, turn around and repeat. Simple. If you do manage to die, just get back to the point where you pick up the Dark Dragon Sword and skip all the cutscenes til you get back to the fight. See this game isn't so mean after all...lol. Now give yourself a pat on the back for finishing one of the hardest games of all time.

One more thing, I am I the only one who thinks Rachel is hot? I may go through the game again on Hard later but I doubt the strategies will be different. I'll post a boss guide for the original Ninja Gaiden mini-games once I get all of those pesky Golden Scarabs.