"We are not inclined to entertain your writ petition. It is better that you withdraw it and approach the income tax assessing officer," a bench of Justices S Muralidhar and Chander Shekhar said.
The order makes it clear that the income tax proceedings will continue in the case.
The court also said that the company has not moved the assessing officer and raised its grievances, so it should first approach the IT department and submit its documents.
Sensing the mood of the bench, senior advocate Abhishek Manu Singhvi, appearing for the firm, withdrew the petition which was allowed by the court that termed it "dismissed as withdrawn".
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Young Indian (YI), which was incorporated in November 2010 with a capital of Rs 50 lakh, had acquired almost all the shareholding of the Associated Journal Ltd (AJL), which is the owner of the National Herald newspaper.
BJP MP Subramanian Swamy, in a private criminal complaint filed before a trial court, had accused the Gandhis and others of conspiring to cheat and misappropriate funds by paying just Rs 50 lakh, through which YI had obtained the right to recover Rs 90.25 crore which the AJL owed to the Congress party.
The firm had challenged a notice issued under sections 147/148 of the Income Tax Act by which the department had sought to reopen a past assessment on the ground that certain income had escaped assessment for the year 2011-12.
The counsel for the Income Tax Department had opposed the petition, saying the firm has not moved the assessing officer and hence its plea was not maintainable.
The trial court had summoned the Gandhis and others as accused persons, besides Young Indian on June 26, 2014.
On December 7, 2015 the high court had rejected their pleas for quashing the summons issued against them by the trial court in the case.
On December 19, 2015, the trial court had granted bail to Sonia, Rahul, Vora, Fernandes and Dubey, who had appeared before it pursuant to summons. Pitroda was granted bail on February 20, 2016 when he had appeared in the court.
Sonia, Rahul, Vora (AICC treasurer), Fernandes (AICC general secretary), Dubey and Pitroda were summoned for the alleged offences of dishonest misappropriation of property, criminal breach of trust and cheating read with criminal conspiracy of the IPC.
According to IT records, 83.3 per cent of Young Indian was held by Sonia and Rahul, 15.5 per cent by Vohra and the remaining 1.2 per cent by Fernandes.