There is no definitive answer to this question as it largely depends on interpretation. In some stories Snake Eyes is enemies with Cobra Commander the leader of the terrorist organization Cobra. In other stories he is enemies with Storm Shadow his former mentor who is now a member of Cobra. And still in other stories he is enemies with Destro the head of Cobra’s arms manufacturer. So really it depends on which version of the story you are looking at.
1.
Who is Snake Eyes’ arch-nemesis?
1.
The Cobra Commander is Snake Eyes’ arch-nemesis.
