Exe likely stands for Exetior and potentially Executor.
― to Exeller when he gave tips to him in Sonic.EXE: Spirits of HellĮxetior (エクセティア Ekusetia) (originally known as Executor and also sometimes referred to as X as a demonic nickname) is the titular main antagonist in Sonic & Exe and the Sonic.exe Nightmare Version series. Tails is weak, but after some time he could defeat you.' ' Remember, be careful with the timelines.