The rivalry between Storm Shadow and Snake-Eyes is one of the focal plot lines of G.I. Joe: Sigma 6. There have been hints and references as to the cause of their enmity. The 4Kids TV website for Sigma 6 states that Storm Shadow was on an infiltration mission in a Cobra base and was captured and brainwashed into thinking the Joes and Snake-Eyes were his enemies. Though Storm Shadow called Snake-Eyes "brother", the exact nature of that relationship is unknown. Storm Shadow frequently blames Snake-Eyes for the downfall of the Arashikage ninja clan..
On occasion, he used Ninja B.A.T.s as support troopers. This is an interesting difference from the A Real American Hero series, as ARAH Storm Shadow preferred highly trained humans as opposed to machines.
In the series finale, "Assault", is Kamakura, rather than Snake-Eyes, who faces Storm Shadow. Even though the resolution of that battle is not seen, Kamakura seems to have been the victor, because Storm Shadow's next and final appearance in the episode (and the series as a whole) is among the captured Cobra members.