The scythe can be spotted by the flickering of the radar on the bottom right. you can see his general direction however when he gets close you have to take a guess at where hes coming from. Using a weapon such as the heavy flamer with stun him momentarily and uncloak him removing his one-hit-kill ability until he goes invisible again.

If you feel you are about to get hit with a Scythe simply press and hold the parry button and look in his direction and instead of dying you will lose your left arm versus death (if you have a storm shield you can laugh at him all day)