I din’t know why I always come back to this character in Joe, maybe it’s because the episode is just so… hell, I don’t know.
I always thought they should have revealed later on that the Viper was actually a trained agent (ala 007) for a foreign government, who had stumbled upon the Cobra intel. The other country being an ally, wanted to get the info to the Joes, without blowing their own agent’s cover, hence they came up with the “Viper”. 