To defeat the empress of time for the last time, dodge all her attacks, especially the kicks. Do not let her get near the girl in red. When only a little of her life remains, keep blocking and press Y or B. A good but slightly cheap way to defeat the Empress of time in the normal ending is as follows. At the end of the intermission sequence, immediately jump backwards towards the edge of the "arena". Simply back away off the edge. It is impossible for her to attack the Prince while he is hanging from the ledge. Shimmy over a few feet from her (she usually will not follow). Anytime you are ready,
simply pull yourself up and do a three-hit combo on her. If she blocks one of the attacks, jump back quickly to the edge to avoid a combo from her. If she slows down time, immediately go back and hang from the ledge until time returns to
normal. Doing so is a good way to save your Sand Tanks until you find a better opportunity to use them. Once you feel like it, use one of your own sand tanks to slow down time. Then use the B(3), Toward, A(6) combo. Once you finish this
combo, jump back towards the ledge. You may then choose to either use the three-hit combo or the Slow Time combo described above. Any time she uses the whirlwind attack, just run away. Using your Sand Tanks to slow time for this attack is not recommended, as it only takes away two to three seconds of the whirlwind. Try to keep all of the whirlwinds away from the camera. By doing this, you can run towards the camera without worrying about hitting a whirlwind. Once the winds are done, repeat the strategy discussed earlier. It may take a while to complete and is cheap, but it is much easier than actually trying to dodge her attacks.