These are the some of the things that I have noticed about the system:
MC can obtain coins from killing and opening chests that are left behind from the corpses of ninja who he has killed. Typically the stronger the ninja that is killed the better the reward he can obtain from the treasure chest. This also corresponds to the amount of coins he can obtain through the killings
The main character can exchange his gold from the killings with the equipment which is in the systems store. Generally the equipment thats in the store are stonger and have fewer restrictions and limitations than equipment he can obtain from killing and opening chests.
Thirdly the MC can obtain the equipment from chests and can synthesize the obtained equipment to create stronger weapons hence increasing his combat power.
Fourthly, the system can give the MC missions with no penalties, these missions are generally related to events which will occur in the story such as missions related to kannabi bridge. These missions can give rewards to the MC.