What's got you confused is the "50% fee", you are thinking this is some sort of tax, and then you pay tax. No. This is a concept called withholding.
Imagine a world with no withholding. Say your wage is $52,000/year. Every week you get your paycheck and it's all your pay, no withholding, so it's $1000. Then, at the end of the year, you do your taxes. Your tax is $5200. So you have to write a check for $5200. Yeah, right, who has that kind of money laying around? I spend it all every check!
So they withhold money for taxes every paycheck, and put that into a your account where it's reserved for paying taxes. It is your money, but it is held/reserved to pay your future tax bill. At the end of the year, you file your taxes. Figure out what your total tax was for the year (say $4000). Then, you apply the withheld tax amount to that number (say $5200). The first $4000 of that pays your taxes, and the other $1200, you get it back! That is called a tax refund.
So in your case, the "50%" is withholding. They are withholding at a high rate for reasons I don't know.
You need to file a USA Form 1040 or 1040-NR taxes. When you do that, you will list this amount under "Tax Withheld", which counts it as a tax payment. If too much was withheld, you would get a refund.