First. Most fringe benefits are taxable, unless they fall into certain specific categories that have tax privileges like medical insurance premiums.
So personal use of a company vehicle is taxable income. The fair market value should be added to your W-2. (For example, if the lease payment on a similar vehicle is $400, then personal use of a work-owned vehicle would be worth $400 a month added to your W-2 taxable income.
It sounds like did not include the income on your W-2 and you did not pay tax on the value of car for 2016. That means you paid much less tax than you should have last year, and he also paid less employment taxes (employer's share of medicare tax and social security tax.)
So for this year he gave you a raise and then took it back for the car he now says he "loaned" you.
There is no way to fix this yourself on your tax return. You aren't repaying a prior year overpayment of wages, for example. There is no way to fix this problem yourself. You may want to see professional about your taxes this year. You definitely should see an attorney because he is breaking several tax laws.
Now in the end, if he does undo this mess and issue a correct W-2 for your 2017 wages without the fake loan, he will also have to issue a corrected W-2 for 2016 that includes the value of the car as taxable income, so you will have to file an amended return and pay more tax for 2016. It may be that the extra tax for 2017 is close enough to the tax you should have paid last year as makes no difference. A good tax preparer could help you figure that out. If it does equal out in the wash, then you might not want to mess with an attorney since, if everything was done correctly, you will owe less in 2017 but more in 2016. If the raise for the "loan repayment" is equal to the value of the car that should have been in your income last year, then the tax bracket shift you see this year is exactly the same as the bracket shift you would see if you filed a corrected 2016 tax return.
And remember, while you owe more tax (or get a smaller refund) -- either this year or last year -- you got the benefit of driving a company owned vehicle which saved you on your own car payments, maintenance and insurance last year.