To get the secret ending simply obtain all 9 life upgrades, when you get to the room before the Empress' throne room there will be a new sword waiting for you. It is the water sword and said to be the only thing that can kill the Dahaka. For your final battle, instead of fighting the Empress you fight the Dahaka.

The Dahaka’s attacks are repetitive and predictable. When far away he will shoot his tendrils throw the ground up at you, run around in circles to avoid it making your way ever closer to him. If you get too close he'll shoot out his tendrils directly at you, roll to dodge them. As you roll slow down time and go in for some heavy combo hitting, as you get him lower in health the Empress will help you and shoot him off the arena, he will be stuck on the ledge, stock up on sand tanks (They regenerate around the arena) and slow down time or use Ravages of time to inflict maximum damage. He'll eventually get back up and jump at you, constantly roll until he calms down and remains stationary. Repeat the same method as before until he is defeated.