The rank system created by Koete, is a promotion to your ninja to take hardest missions, have the access to another places, buy some strange items and etc...

First of all you need pick a mission in the board.

Then, you can check you mission in Status/mission. All information about the progress of your mission is there.

When you done the mission you can go to the Kage's acessor and report it saying {mission, reward}.

According to the points you earn you will increase your ninja rank.