XL. Boss Battle - The Mysterious Warrior
This takes place in 2D, and all you can really do is fight and block. If you get backed into a corner, jump over your opponent and attack from the other side. You'll eventually get the chance to shove him through the glass.
XLI. Boss Battle - The Kraken
Ugly beast, isn't she? OK, first off, head to her left tentacle and attack it until it raises. Go to the middle, pick up your fallen buddy, and plonk him on the button to activate the fan. You can now attack the creature's face, so float up and combo it. Repeat the process until the Kraken slams her tentacles into the fan. When she does this, climb up the side and slice it off at the joint. Repeat with the other tentacle.
Now the Kraken is hanging on for dear life. Put in a couple of combos on one tentacle, then move to the other. You've now softened them up. Return to the first tentacle and beat it until the Kraken lets go of one pillar, then sprint to the other side, and dislodge the other tentacle. Now run to the middle, pull the lever, and send the bridge through its face.
XLII. Taming the Phoenix
Grab the Gorgon Eye and Phoenix Feather from the chests. Press Circle next to the Phoenix and you'll need to go through a Quicktime event. Be careful here. If you miss a press it'll take health from you.
Puzzle focus - Temple Of The Fates
Swim up to the middle platform and press R1 to grapple up. Drop down and smash the gem to return the room to normality. You can now ring the bells to smash the giant face in front of you. Firstly, head over to the right hand bell and use R1 and L1 to ring it. Freeze time, and leap onto the centre platform. Use R1 to kick the ringer into the left-hand bell. Repeat this once then drop down into the water. Dive down under the centre platform and pull the lever to lock the platform into place. You can now use the crank on the surface to turn the bell ringer towards the giant face. Now hop back up and use the ringer to smash the face.
XLIII. Temple of the Fates
Head through when you're ready, although if you fancy it, there are some crates behind and to the left of the central platform, which you can reach by grappling up and gliding - although they're tricky to get to.