Storm Shadow has always and only been a "good guy". He is often portrayed as a cobra for marketing purposes or selling toys, comics, and merchandise, although in the development of his character, it is usually always the playout that we learn that he is a good guy fighting for the bad guys for some unknown reason.

In the original Marvel "Canon" series, Storm Shadow went undercover inside the Cobra organization to discover the facts behind the murder of his uncle; which he believed had Cobra ties to it.He was never truly a bad guy, but merely a cover agent working on his own agenda. He later discovers the identity of his uncles killer and leaves the Cobra organization. He only returned once to the dark side of the Joe mythos during the end of the 155 issue run, when he is captured by Cobra Commander and put under the brainwave scanner.

In alternate universes, Storm Shadow is seen working for Cobra, but usually his character is revealed to have an outstanding sense of honor and mystery, and we are always left wondering what his true motives are. He never truly fits in with Cobra, but because of sales and marketing strategies, he is most often placed there.