(a) The provisions of this chapter shall apply to any eligible taxpayer who files an application for amnesty within the time prescribed by the commissioner and does the following:

(1) Files such returns as may be required by the commissioner for all years or tax reporting periods as stated on the application for which returns have not previously been filed and files such returns as may be required by the commissioner for all years or tax reporting periods for which returns were filed but the tax liability was underreported;

(2) Pays in full the taxes due for the periods and taxes applied for at the time the application or amnesty tax returns are filed within the amnesty period and pays with the taxes the amount of interest due and pays the amount of any additional tax and interest owed as may be determined by the commissioner within 30 days of notification by the commissioner; and

(3) The commissioner may, in his discretion, impose by regulation, the further condition that, in addition to the requirements set forth in paragraphs (1) and (2) of this subsection, the requirement that any eligible taxpayer also pay in full within the amnesty period all taxes previously assessed by the commissioner that are final, due, and owing at the time the application or amnesty tax returns are filed and pays with the taxes the amount of interest due and pays within 30 days of notification by the commissioner the amount of any additional interest owed.

(b) An eligible taxpayer may participate in the amnesty program whether or not the taxpayer is under audit, notwithstanding the fact that the amount due is included in a proposed assessment or an assessment, bill, notice, or demand for payment issued by the commissioner, and without regard to whether the amount due is subject to a pending administrative or judicial proceeding. An eligible taxpayer may participate in the amnesty program to the extent of the uncontested portion of any assessed liability. However, participation in the program shall be conditioned upon the taxpayer's agreement that the right to protest or initiate an administrative or judicial proceeding or to claim any refund of moneys paid under the program is barred with respect to the amounts paid with the application or amnesty return.

(c) The commissioner may enter into an installment payment agreement in cases of severe hardship in lieu of the complete payment required under subsection (a) of this Code section. In such cases, 25 percent of the amount due shall be paid with the application or amnesty return with the balance to be paid in monthly installments not less than 25 percent of the original amount nor to exceed three months following the expiration of the amnesty period. Failure of the taxpayer to make timely payments shall void the terms of the amnesty program. All such agreements and payments shall include interest due and accruing during the installment agreement.

(d) If, following the termination of the tax amnesty period, the commissioner issues a deficiency assessment based upon information independent of that shown on a return filed pursuant to subsection (a) of this Code section, the commissioner shall have the authority to impose penalties and criminal action may be brought where authorized by law only with respect to the difference between the amount shown on the amnesty tax return and the correct amount of tax due. The imposition of penalties or criminal action shall not invalidate any waiver granted under Code Section 48-16-6.