Shisou comes from a large and rather famous family, at least famous in the underworld of Japan.  For a long time the Kobayashi family has been praised for raising strong martial artists... oh who are we kidding here? Ninjas!  They have a long history of ninjas-- or lack there of-- because well-- a good ninja can't be traced back to their family.  Point is, the people who know how and where to hire such a person knows the Kobayashi family used to be the place to turn to. That was, until a mission that ended in horrible failure, lead by Shisou.

Shisou came back empty handed, and he blamed the only other ninja known to have survived whatever had occurred at the place of his target: his rival, Tom, an American kid that was extremely skilled at everything he did.  Shisou had to work hard to be as good as he is now but Tom always seemed a step ahead of him.  He was even allowed to work as an outsider for a rival family with only a few months of training, something that Shisou broods over, and hasn't forgotten.

Shisou's grudge hasn't been completely lifted even now- as Shisou helps Tom prove he had nothing to do with the failed mission-- and also to help defeat the ones who were behind it, the Magi of Power.  Shisou is currently engaged to the beautiful but sometimes overpowering Naoko, who is quite possibly the most gifted priestess since before the sealing of magic.