From the Wikipedia article on Hattori Hanzo:

He died at the age of 54 or 55 in 1597. There are three theories about his death. One asserts that he was assassinated by a rival Samurai, the pirate Fūma Kotarō. After Hanzo tracked him down to the Inland Sea, Kotarō lured him and his men into a small channel and used oil to set the channel on fire. The second theory is that Hanzo became a monk in Edo where he lived out the rest of his days until he died of illness. The third theory is that he died because of illness and it was a natural death.