When you can’t see your target you take either a -30 or a 50% chance of missing no matter what you roll. That means that it you have a 59% or lower of hitting your target unmodified, you are better off taking the 50% miss chance... seems weird that the “worse” penalty is sometimes the better option.

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Yeah, that does seem odd. It has echoes of Shadowrun's 'sometimes it's better to blindfold yourself before battle' issues. Probably easier to turn the 50% to a flat -50 penalty, or apply that -30 /in addition to/ the 50%.

Yep. Pretty much...

The interactions with Fray make this a little more significant. Against a Fray of 80 (halved to 40), if your skill roll is 66, you have a 57.47% chance of hitting. With a -30 penalty, you have a 28.65% chance of hitting. So even with a skill roll of 66, the 50% miss chance is better than the -30.

I'm a fan of stacking the penalties. You could have the GM determine which to apply, but since the math is a bit tricky, and the GM has enough on his plate, I'd rather just say you get both penalties (-30 and 50% miss chance).

Edit: Fixed my math