the Yiga base is a long and tedious journey. This base consists of Yiga blademasters who hold torches. you have to make it through the base without anyone seeing you. once you get to the end you have to fight Master Kohga and recover the thunder helm. They store there stash of mighty bananas there.
In the 2nd room there is a secret place with some rupees. If you burn the banners down once the base is cleared then you get in to it. there are also some treasure chests underground in room 3 and a secret door to master kohga.