Unknown
No one completed stage 2 this time, so we didn't get to see any of stage 3. They did show a quick shot of one new obstacle in the episode intro. It looks like a staircase that goes up and then down. If this were Women of Ninja Warrior (Kunoichi) I'd guess the steps wobble back and forth, requiring competitors to balance as they climb. For men's Ninja Warrior, I don't know ... maybe they have to hang from the steps? 
This obstacle is known as the Devil Steps. Rather than climb on the steps, the competitors use their arms to "climb" the inside part of the steps. They climb facing the steps so at the apex they have to turn their body in order to get down.