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Just block her attacks. She finishes each sequence by thrusting both swords up, then doing a cross-slash. Counter-attack after the final slash. Keep up your attack until she starts blocking, at which point you should starting blocking again. Be ready to mash the attack button when your swords lock.
You need to vault over him as you attack, otherwise, he'll block. Be careful about positioning or you can vault right over the edge to your death. Block his attacks, then jump over him, hit him twice in the air and hit him in the back as many times as you can before he turns around and starts blocking. Go back to blocking at that point and wait for another opening.
Shadee second encounter
Shadee is harder this time. Some of her combos have unblockable moves, so you should try to keep your distance rather than blocking. Other than that, use the same strategy as before. If you run low on sand, check the pots near the edges of the altar.
From this point on, do not attempt to fight bosses in real time. Slow time, then hit her as much as you can while it lasts. Vaulting over her with two air-strikes, followed by a four-attack combo to her back is probably the quickest way to do damage. Start slow-time up again as soon as it runs out. When you have her down to about 2/3 and 1/3 health, she stops the fight and summons minions. Either vault them and attack or slow time on them as well. They will replenish your sand tanks. After this, wait until the empress comes back down off her floaty sand thing to slow time again so you don't waste your sand. If you run out of sand, there is some in pots at the edge of the throne room.
As soon as the cut scene ends, start charging Cyclone of Fate. You should be able to hit the griffin with three tanks. Start charging it again as soon as you recover and hit him with another three. Next, he will go into the air and start dive-bombing you. Run perpendicular to his path and roll as he folds his wings to dodge this attack. He'll do this several times, and then start to land. Get in his general vicinity and charge cyclone of fate again and you can hit him with another three tanks as he lands. This time, he'll stay on the ground. Slow time and attack his legs until he goes in the air again. Repeat slowing time and going for the legs when he is on the ground, and hitting him with cyclone of fate as he lands until he is dead and gone.
Empress second encounter
The Empress is much more difficult this time, but the same basic strategy still applies. Slow time, and then attack her. Keep doing this. Never attempt to fight her in real time. When she's at about 2/3 and 1/3 health, she will summons some sand storms. Run around and roll to avoid these. They do considerable damage. They will die out after a bit and leave sand tank recharges. She then goes back into normal attack mode. Repeat the same strategy from before.
As always, slow time. Try to keep him from facing you. If he turns to face you, roll sideways and keep attacking. When approaching him for a distance, he'll try to do a tentacle attack. Block and roll sideways to avoid damage until you can close the gap. After he's down to about half health, he'll got knocked over the edge and hang there. Run up to him and combo at him as fast as you can. Start the slow-time up again as soon as it runs out. You'll have better luck if you have a secondary weapon. He'll get back up. Repeat what you just did. You should be able to kill him the second time. Make sure to pick up the sand as it appears or you won't have enough to finish the fight.
(Note: all life upgrades are in the past)
Near the bottom of the main fortress entrance stairs (in the past) there's a raised area with another staircase on it. When facing the staircase and standing at the bottom, there will be some barrels to the left. Smash the barrels to reveal a switch. This switch opens the rat-trap gate at the top of the stairs. It will close before you can get to it. It is possible to reach it by jumping over the stair railing, then rolling all the way to the hole, but it's much easier to just come back after you get Eye of the Storm. You won't really need extra health before then, anyway.
There is a large stone object in the center of the upper platform, just up from where you fight Shadee the second time. Grab it and pull it toward the stairs and the wall will open. Try to get this as soon as possible. Coming back to this area at the end of the game can causing game-stopping glitches.
Turn the switch in the central hall so the gap in the floor is filled. On the west side of the walkway, there is a place where you can drop off the edge, then wall jump to a lower area. Run along the wall, then jump near the end and wall jump up the top of that structure, and then run on the next wall and wall jump down until you're hanging on the ledge. You should be able to jump across and shimmy around to the platform. The life upgrade is through the door.
There is a gap in the railing in the room with all the trees. Jump through it and you can shimmy along a ledge to get to a tunnel that contains the upgrade. Get this as soon as you can as it gets sealed off late in the game.
Water Switch Room
Wall-run up to the ledge in the room that contains the switch you use to turn on the water.
In the big room where you fight the third golem and activate the clock tower, there are several breakable walls. When standing in the entrance and facing the golem, there is a switch and save fountain on your right and a life upgrade on you left. Stand in front of the wall, and then wait for the golem to throw explosives at you. Alternatively, you could come back after getting the scorpion sword and break the wall yourself.
In the room above where you get the scorpion sword, there are two breakable walls. Break them both, activate the switch in one, then use Eye of the Storm and run tot the other. You only go through this area twice and you can't come back, so be sure get it when you can.
When you're walking on the big donut-rings above the library, you can jump to some ledges in the wall from the second ring. Shimmy to your right to reach the door to the upgrade. You must get this your first time through as the ledge become impassible later.
There is a breakable gate on one of the platforms on the top floor of the antechamber in the southern passage. After you get the Scorpion Sword, come back, break the gate and drag the block out onto the platform. You can use it to wall-run to an area above the platform where you can find the final upgrade.
Glitches and work-arounds
Sometimes, after the first Shadee fight, you will load your game to find yourself as the Sand Wraith. He's dressed all in black, has glowing eyes and loses health. If this happens, you cannot continue in the game, as a necessary cut scene won't be triggered. You must revert to an earlier save.
Sometimes after restoring from a game saved in a portal room, the prince will only be a floating head and weapons. This is a harmless glitch and doesn’t keep you from progressing.
If you get all life-upgrades as early as possible (meaning before the mask of the wraith), when you enter the hourglass chamber, the cut scene from before you fought the Empress will play again and a boss health bar appears. You can still go through the same hallway you normally would, but it dead-ends. There is a work-around, though. Head right at the end of the hall and you'll glitch through the wall and appear in the throne room. The Empress is there, but you can't fight her. Smash the back of the throne to gain access to the time portal. Go in and save in the portal room before going through the portal. When you go to the present, there will be no room, only black space, and you'll fall to your death. If you select "retry" on the game over screen, it will work correctly the second time, however. After this, the game should continue as normal.
Sometimes, at the end of the game, you will not be able to go through the portal behind the throne room. It is unknown what causes this and there is no work-around. You will need to go back to an earlier save.
In the first Empress battle, the prince sometimes gets stuck in the floor, and then drifts into a wall and dies. Just retry. This isn't a persistent glitch.
Liquid Floor 2
In the second Empress fight, if she uses a teleport attack while you are hanging off the edge, she can get stuck in the floor. There is no way to damage her, so you'll have to kill yourself and retry.
Liquid Floor 3
When returning to the room in the mechanical tower where you activated it late in the game, the final gear shaft sometimes become impossible to stand on. The prince will fall right through it. The same is true of the floor on the other side of the window. It is possible to wall-run to the window, jump from the window to the artwork chest and jump from the chest to the other ledge and thus get down anyway.
Also when returning to the activation room in the mechanical tower, it is possible to fight the golem without him stepping on the platform. If you beat him, it will raise a level whether he's on it or not, however and can end up blocking your path, though you can still get out via the other route by swinging on the gear shafts.
When returning to Dahaka chase areas, sometimes the screen will turn sepia again and tentacle effects will appear. This is a harmless glitch. Play can continue as normal.
If you return to the sacrificial chamber after completing the Sand Wraith Segment, you cannot leave. You aren't supposed to be able to get back out the way you came and if you attempt to leave the same way you did before, you will find that it is no longer possible to grab the ledge in the present antechamber you used to escape this area the first time. The prince simply hits it, and then falls to his death. There is no workaround. You must restore from a save before you entered this area. If you don't have the life upgrade in this are yet, there is no way to obtain it.
At the end of the sand wraith segment, if you go back into the library rather than leaving the mechanical tower, scripting is broken and when you do attempt to leave, the platforms will be in the wrong position and no cut scene plays. If you restore a save at this point, you are back to being the regular prince instead of the wraith. There is no known work-around.