I think the Moon Temple and Twin Labyrinths belong to the "darkside". Read their save tablets so you'll have them activated later when you find a way to warp to the darkside.

The grapple gloves are just for clinging at the walls (and jumping off of them) They're usefuly in a few places, especially in sections where you fall. Using them effectively you won't waste seconds crushed on the ground anymore. I always wondered if there's an upgrade so that you can actually climb (as a skeleton in the Sun Pyramid suggests), but that's one thing I still have to discover.

I had tons of trouble with Bahamut. I was able to beat it with a good use of Flare Gun and Axe. It is rather easy when you learn its pattern. It's entirely possible to beat it without taking any damage.

Edit: ok, forget this fish. Some questions. I saved in twin labyrinths and some moon temple. I can't warp to either though. Is there a way to? Also, I got the grapple things, and the description says I should be able to scale walls, but I can't actually scale them, just cling and then either fall or jump straight across, never gaining height. Am I doing it wrong?

This warping issue was the reason I quite playing the original. I thought it was a bug but as I played the remake I found out that you need to find a certain software and plug it in the computer to be able to warp to those levels too.

I think it's not possible to climb up the walls. You'll need it in some points to be able to get up though. You use it by jumping, clinging on the wall, jumping to an upper ledge, and doing it again to get even higher. So, you can use it to get higher but not in a way you'd first think.

Not sure I understand your explanation of how to gain height with the claws, but it'll probably hit me when I arrive at such an area.

There is a room early on in the Egyptian area where you can't reach it from a jump, but if you try falling from above, it's just barely unreachable... or so I thought. I saw in a speed run linked here the guy just fell and maneuvered easily to land on the ledge. It's the room that's not lit up initially to the left and down from the entrance. Any help on that one, or is this area even essential? I like to watch until I see something I can do... then I go do it, rather than sitting there and spoiling everything, so I'm not sure what awaits me aside from a glimpse of a subboss.

And yea, Bahamut looked like a reasonable boss in that Let's Play when using the flare and axe... sadly, two items I have yet to find. Could really use the flare since I found the dark area. Exploring without it has been futile... and scary.

If I understood correctly what room you mean, there is a way to make a light appear. The Flares aren't helping there (in fact I think you can't even get the flares before that).

When you've made the light to appear in that room, you can see some previously invisible platforms. The easiest way to land on one of them is to use a certain type of a jump what allows you to move around while falling. To make this jump you must jump straight upwards and when you are in the air you can start moving the character to whichever side you want him to go, and when you drop down using that method, you can steer the character in the air enough to make it possible to land on one of the platforms.

That style of jumping is very handy in several situations. Whenever you think you should have more control in jumping (like perhaps a situation where you might need to jump only a little bit forwards), just jump upwards and press left/right while in the air.

The "mechanism" that makes the light appear is close to that place, if you haven't already found it.

I already had the light activated but didn't notice platforms when laying or watching. The speed runner just jumps like you described and lands right in the entry way to the next room. Ill have to give it another look after work.

The red lights themselves are the platforms. That's one thing I stumbled upon by accident, because it doesn't look like you can stand on them.. Some bodyparts of the giants too...
Anyway, the mid-air jump Airola mentioned is extremely helpful in this place.

As for the grapple, I think there are moving platforms later. you can grapple onto them from the side, and they'll take you upwards.

Like others have said, use the jump then move technique. I use the wide channels in the background to line the jump up. The channels are visible in both the upper and lower screens, and line up with the edge of the platform on the far right.

It took me a while to get my system down, but failing over and over allowed me to get real good with my stabbing knife. That knife is essential for taking out the cat and two birds on the upper screen. stab stab stab! Stabby knife!

The jumping method was not the problem. I didn't realize that the lights were platforms. I was trying to land directly on the edge because I saw someone do it in a video and assumed that was the main method of doing it.

This is one of many instances where I had the right idea at the beginning but then decided it was a waste of time to try or just forgot that I hadn't already tried it, because I definitely had the idea that the lights were platforms earlier.

Anyway, thanks for the help as usual, guys.

POSSIBLE SPOILERS

Well, I think I finally reached my breaking point. 13 hours into the game (more counting deaths and resets) and I'm completely, utterly stumped. I did manage to get relatively far, though, never once touching a guide. I found and defeated four bosses (Amphisbaena, Sakit, Ellmac and Bahamut, in that order), I stepped into and explored quite a few areas of the game and discovered several secrets, all on my own, never reaching for external aid. Heck, I even figured out (by sheer chance and a massive stroke of luck) the supremely obscure puzzle that leads to the Fruit of Eden, on my own! In fact, here's a screenshot of my inventory screen at the time of writing this: http://www.rphaven.org/gs/stuff/lamulana.jpg

Well, I think I finally ran out of luck. By now, I've wandered throughout the entire place and revisited every room I have access to more than once, trying anything and everything in each. But nothing seems to work. The Endless Corridor is still only four rooms long (the map shows 12 more rooms), the Chamber of Extinction is still dark and the 4 rooms at the top-right corner of the map continue to be seemingly inaccessible to me, the miniboss at the bottom of the moon pyramid continues to be invincible, In the Twins' Labyrinth I found the Ankh but not the jewel, and I can't do anything but pointlessly wander back and forth in the first corridor of the ruined "Eden" area.

So yeah. I have to admit defeat, which sucks and I hate it, but what else can I do?
It looks like I have to... (shudders) ...check a guide, for the first time.

Well, there goes my pride as a gamer...

You're in good company.

Well, like I said earlier, I looked for some help. Since Deceased Crab is now Let's Playing this version of the game right now, I decided to check it out for a little... guidance (hohoho... see what I did there?).

Some of the things I missed were my own fault, sure, like the whereabouts of the item I needed to beat that miniboss at the bottom of the moon pyramid. I really have no excuse for not finding it on my own. But then there was stuff like the location of the axe... Or the puzzles in the Gate of Confusion. Those really are something else. Honestly, quite a few of the puzzles in the Gate of Confusion are so obscure I just don't think they can be realistically "solved" without external aid. I mean, the ladder one near the beginning of that area is particularly notorious in its sheer randomness. And, unless I missed some random tablet somewhere, I don't think there was any clue about it at all. How are you supposed to figure that one out?

Well, at least I made a lot of progress today, but I have this foreboding feeling things will only get harder and more obscure from this point on...

beat the Giant boss. Definitely easier than minecart boss, especially when I stopped being dumb and impatient for the first form. I haven't found any new weapons or roms in the Mausoleum or Temple of the Sun and I'm worried about this.

I already beat the whole game without a guide.

You mean you obliterated Sakit, but the adventure continues!
Also, I found that the best strategy against Ellmac is to stick to his face and whip it until he dies. A heck of a lot faster than using shurikens, which takes forever. I also faced him after finding quite a few life orbs and the first whip upgrade, which was super effective, so to say.
Anyway, there are some weapons in the Mausoleum of the Giants and the Temple of the Sun that can be obtained relatively early. One of them involves ghosts and the other involves shurikens and marksmanship.

I know the latter, I'll eventually figure out the former.

I finally completed the game with all items, software, etc... Took 23 hours though
Kinda sucks that not all of the music is in the "Jukebox" (only 51 tracks, with both music EXEs).
Now to try to complete the game without watching the play-through videos when I get stuck.

Well I have managed to beat 5 guardians all on my own without looking at a guide, but the past couple of days I have basically been wondering around with absolutely no clue what to do. I'm 24 hours into the game and really don't want to admit defeat and look at a guide. I've actually been holding off on reading this thread in fear of reading some spoilers, but I decided to check and see what you guys had to say about the game. Looks like I activated hard mode without realizing it . No wonder I was stuck on Viy for a couple of days. Turns out I didn't see anything I didn't already know (other than the hard mode trap), so maybe that's a sign that I should give it a little more time before reading a guide. It is comforting to know that many of you here are stumped as well.

One other "trap" that happened to me was I went down to the Temple of the Sun before I got the boots or the Holy Grail and I saved my game there. Without the boots you can't climb the sand slides and I couldn't leave without the Holy Grail, so I had no way to escape and had to completely restart my game. Luckily I was only an hour in, but still it was frustrating.

You defeated Viy? You might want to revisit the waterfall area at the surface...

About exiting the Temple of the Sun without Grail/Boots, it's actually possible. You have to make your way back to where the switch to turn on the lamp used to be (that's inside the structure right below the exit to Gate of Guidance). There's a breakable wall to the left of one of the ladders in that small enclosed area. It disables the stone pillar blocking the exit.

EDIT: Oh. I think I should also share this.

ITEMS ALMOST LOST FOREVER:
-Item to the left of Pazuzu's room in the Inferno Cavern. Save before attempting. Don't save if you fail.
-Item obtained by solving the Scales of the Heart puzzle. You only get one try. Save before attempting. Don't save if you fail.
(You can reset these puzzles somewhere in the ruins... good luck finding that place without a guide, though. It's just easier to save before attempting them)

ITEMS DEFINITELY LOST FOREVER:
A piece of software in a chest in Shrine of the Mother. Not easy to miss. It's almost in plain sight. Get it before defeating all 8 guardians.
A Life Orb in Shrine of the Mother. Very hard to miss. I mean, come on, it's right there! Also get it before defeating all 8 guardians.
A Life Orb in the Dimensional Corridor. Get it before defeating the dragon miniboss (Ushumgallu, check the map). Also: Hardest. Life Orb. Ever. You have no idea...

Potential Spoilers:

Yeah, I found the Tower of the Goddess under the waterfall, but there doesn't seem to be anything I can do in there. One puzzle in there says I need a golden key but I don't have that yet. The exits on the right hand side of the tower are blocked by statues. And strangely, the headless statue at the bottom of the tower on the right side has a secret room on her back, but it is empty. I'm guessing at some point, with the right item in hand, that will change.

There is also a puzzle in the twin towers that has me stumped. I found the ankh after the witches puzzle, but there is another puzzle that says to shine the light on the twins and then shine the light on the ruined world. I figured out to shine the light on the twin's statues, but I have no idea what is implied by the ruined world.

And then there is the Eden puzzle, which is just beyond cryptic. Welp, I'm off to look at a guide. At least I can be proud I made it this far without a guide, right? lol

EDIT: (Still Spoilers)
After reading the guide, there were two things I probably would have never figured out on my own. One was going down the pipe in the Giants land where the statue is pointing. I knew there was something to do with that, because a statue mentioned something about "Where the finger points", but going down the pipe was something I probably would have never guessed. Also, buying 20 weights in the little brother's shop in the twin towers to open up the big brother's shop would have never occured to me. I get that this game is a throwback to a time where games were very cryptic, but some of the puzzles here are just ridiculous lol.

Heh, yeah. I did do the "where the finger points" one on my own, but it was a stroke of luck. I pressed down by accident and was surprised when I saw what happened then, heh.

About the other one, there was a hint somewhere: "Big Brother's shop is for regulars" or something like that. Pretty straightforward hint in hindsight. But yeah, I couldn't figure out that one on my own. Not to mention I mistook a different shop in the Labyrinth for Big Brother's shop, so yeah, I was completely off the track on that one. Oh well. =P

Anyway, if you think these are obscure, wait until you go to the Gate of Confusion...