The fairies are always at the very top of the tallest towers.
I don't remember the specifics, though.
Look for grapple hook points in the outer corridors from the main room.
I'll explain where to go for this, but let me play the stage first (you'll probably be done with it by the time I type it up but I'll put it up for others).
From the room with the three fairies' plates:
1. walk left from the left magic plate on the wall, back where you climbed in on the warg. It's subtle 'cuz the sun is blocking it, but there's a hook-point there. When you swing there, you'll swing back out of the tower and you'll spot another hook point. Grapple to that one and climb up the tower to get this fairy.
2. Solve the puzzle of the fairy plate panels, and you'll rotate the big statue outside on the right, allowing you to grapple across:
Puzzle Solution:
Left-Blue, Center-Red, Right-Red
In this room you'll spot a "wheel switch" on the right wall and a blocked door. More on this later, but for now, walk out the left exit and you'll spot a pin for a wheel switch on the wall. Pick up the pin, place it in the switch and start rotating and STOP 'cuz a Greater Lycanthrope will come out (you'll have to kill it 'cuz he'll keep on interrupting your turning of the wheel switch). Kill him and rotate the wheel to lower the gate.
NOTE: This pin can be removed after this is done, and is necessary to work with the other wheel switch that was mentioned before.
After the gate lowers, you'll spot a grapple point. Swing across to the other tower. There's a grapple point in the ceiling. Grapple on to that and maneuver the platforming to the top of the area (when you make it to the second highest section walk towards the camera for a Brotherhood Knight; if you spot the fairy, you've gone too far, just go back one platform and walk towards the camera).
After you get the fairy, you walk towards the platform on the other side of the tower. It'll turn into a grapple point. Rappel down and when you spot another grapple point, you can just platform in that room to the Brotherhood Knight inside. Get back outside to the platform, and go back to the grapple point, rappel down and you'll reach another Brotherhood Knight on a balcony in front of the big statue you rotated a bit ago.
3. Remember that wheel switch with the pin? Return to the same spot, remove the pin from the wheel switch, and carry it to the tower that had the wheel swich and the barred door on the right side. Put the pin in place, work the wheel switch (no lycanthropes this time), and the barred door shall open. Climb the outer walls of the tower to reach the third fairy.
You can do #2 and #3 in any order. Some people spot the other wall switch first and go there first, and deal with the Greater Lycanthrope later. But most people will spot the switch that's right by the pin first.
Also, if you guys figure out a solution to something, and can express it in a few words, post it! Someone out there may be stuck on the exact same spot and might need that same clue. So while "nevermind I got it" works, something like "nevermind I didn't spot that other switch with the pin" would be a bit more helpful. Just a heads-up for others in the future.
Yeah it took me a while to see that one. I would even push against the edge and tried both a DashTackle and a FalconPunch and neither worked. They really should've put like a glimmer of light or something to tip you off. It was really well-hidden.
It was either lazy or a bad idea. Hey I have a question about the last boss...
DO NOT LOOK AT THIS IF YOU DON"T WANT GAME RUINED
I mean the last last boss, you know what I mean. How do I get past those rings he puts up when he's stunned. Do I just switch back and fourth from light to dark? I keep trying that but I can seem to switch w/o getting knocked back.
Anyhoo, thanks for all your help.
To make things easier to understand, simply switch to the magic that corresponds to the barrier you want to pass. You're free to switch between whatever magic you want while you're INSIDE the circle. The only thing that will push you out are the barriers.