The Rogue System is a system devised as an alternative for missing-nin within certain villages. This allows for a way for them to be active without necessitating the need of actual missions. Below you can see a map of Amegakure and its 5 give regions. From here, the given system can be further illustrated.
As said before, and can be seen to the left, Amegakure currently hosts 5 given regions. These regions all have a number of regular shinobi wandering through there as to perform specific duties like: Missions, Border duty; etc. The presence of shinobi within a region increase its given 'Heat.' Some are high and some are low, each with their own unique amount of shinobi overall which can lead to some in a way predicting the movements of the shinobi.
Further on about what and how Heat works, it signifies the presence and given power of the shinobi at hand. This means that a place with more heat will not only create more chances of conflict, but also it will make things harder for a missing-nin to avoid.
Whenever a missing-nin is put through a lottery and their number is pulled up then it is that they receive a 'Confrontation.' These confrontations are where missing-nin will have a run in with a shinobi squad, the number and power dependent upon the state by which a region is in. A number of options will be presented to the missing-nin on how they may handle a situation, ranging from: Killing, sneaking around; etc. Sometimes actual conflict is unavoidable, as a missing-nin's infamy grows then it is that they're sought out by authorities.