There are few people that do not know about the ninja or the art they used, ninjutsu. However, that does not mean that the impression they have is the correct one.

There does not seem to be any one source for the  origin of ninjutsu. Although the legends of the ninja traditions sometimes talk of Chinese sources, there is little reason to think of this as anymore than a myth that rose up in the same way that stories about King Arthur rose up in England.

The birthplace of ninjutsu was an area in Japan called Iga with its neighbor Koga to the north. The region was close to the capital, but not that close and in an area difficult to travel through. Immigrants from the mainland were settled there by the government and added unique aspects of their culture to the region. Warriors from the defeated side in battles to control the capital of Kyoto fled there. Greedy landowners  that owned land, but did not live in Iga, drove their tenants to revolt from time to time. All these influences mixed to form a unique art. In the aftermath of the breakdown of the Ashikaga shogunate the region was left alone to rule itself.

The people in the region formed alliances with each other and set up a crude form of democracy. They were able to enter the service of warlords outside the area and were often counted as vassals of them. The rule they followed was that they could not serve a warlord that was thinking of attacking their homeland. This and other factors led to the ninja homeland largely being left alone during the age of wars and allowed the ninja to serve all over the country.

The ninja were mainly used as gatherers of information. They would travel in costume into an enemy territory and quietly gather information. They learned to estimate heights and distances by use of math formulas and knew how to subtly ferret out information from people in conversation. Psychology was a speciality of the ninja and they used it to turn loyal retainers against their masters and provide them with inside information.

They are most famous for their use of stealth. When it was needed, they would sneak into areas and gather the information they needed. This was also a useful skill they used during sieges when they  would sneak into besieged fortresses and set fire to things.

Despite how they are portrayed in fiction, it does not look like they really were assassins. There were many, many assassinations during the time, but it was very difficult to pull it off against a warlord. Most assassinations seem to be carried out by a large group of warriors ambushing the warlord and his guards, not a small band of stealthy ninja.

The fighting art of the ninja differed from typical samurai arts in that is was geared toward escape and not killing the other person. If a ninja was discovered by a guard, he had to escape before more guards rushed to the commotion.  They could not stick around and try to defeat someone. The moves they used were designed to prevent pursuit. Blinding powders were thrown in the eyes, spikes were dropped behind them and throws were meant to knock people to the ground to give time to escape. Standing and fighting with a sword was not an option they liked.

Having survived, even thrived, in the most violent periods of Japanese history the arrival of peace signaled the beginning of the end for the ninja. With Japan unified under the Tokugawa shogunate they no longer needed to enter enemy territory.

Their art withered and was tossed aside. A handful of arts were absorbed by other arts and passed down as a form of tradition that might be needed in the future.

Today there are many people claiming to be the inheritors of ancient ninja traditions. Sadly most of them are frauds. The only art that can prove it even existed prior to the person claiming  to have learned it is the tradition headed by Masaaki Hatsumi of the Bujinkan. Along with other arts such as Takagi Yohshin ryu jujutsu, it is taught to a few students in Noda, Japan and in some dojos (training halls) around the world.