Allowing the petition, the Court held  that the reasons given by the Central Board of Direct Taxes for refusing permission were not sustainable. The National Company Law Tribunal, while ordering recast of accounts has kept the rights of the Government to continue with the proceedings pending before the Serious Fraud Investigation Office, Enforcement Directorate and Central Bureau of Investigation. Unless the Income-tax Department permitted filing of the return of income based on the recast books of account, it would not be able to examine the veracity or the genuineness and correctness of the claim of the assessee nor be able to examine the complicity of the former key managerial personnel and their impact on the assessment as well as other proceedings.  That only when the returns of income based on the books of account revised by the auditors appointed by the Ministry of Corporate Affairs were allowed to be filed and examined, could the assessment orders be passed under section 143(1) or 143(3) or reopening of the assessment under section 147 be considered. That when by the order under section 130(2) of the Companies Act, 2013 passed by the National Company Law Tribunal on an application filed by the Ministry of Corporate Affairs and the accounts had been recast and accepted by the National Company Law Tribunal and also filed with the Registrar of Companies under the Ministry of Corporate Affairs, the Department could not raise frivolous objections and hold that the delay in filing the returns of income based on the revised books of account should not be even be condoned. That the assessee could file before the jurisdictional Assessing Officer physical returns of income based on books of account revised under section 130(2) of the 2013 Act, as taken on record by the National Company Law Tribunal for the assessment years 2015-16 to 2020-21 within the time stipulated in this order. The Assessing Officer was to make assessments in accordance with law considering the revised returns of income filed based on revised books of account for these assessment years. Hence, any assessment order passed under section 143(3) or 144C for any of these assessment years for which the revised returns of income had been filed were set aside. Consequential notices issued and orders passed, if any, were also set aside.  That accepting the revised returns of income based on the revised books of account would not absolve the concerned other authorities from any action that should be taken on the basis of earlier books of account based on the ongoing investigation. If after the investigation, these revised accounts were required to be recomputed, the assessee could not raise the issue of limitation for a period of three years from the date on which the assessment order was passed. The calculation of time for the period of limitation provided under section 149 would commence from the date the assessment orders were passed for each of the assessment years. The pending assessment proceedings for the assessment years 2021-22 and 2022-23 could not be proceeded with until the assessment orders were passed for the assessment years 2020-21 and 2021-22. (AY.2015-16 to 2020-21)