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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.
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.