Justice Sonia Gokani rejected the larger conspiracy charge, saying that it was not accepted by the Supreme court.
"It (larger conspiracy) was already discussed by the Supreme Court in Sanjiv Bhatt's matter and dismissed by it. I do not want to go into that, therefore I reject this plea for larger conspiracy," Justice Gokani said.
However, she said that the petitioner can approach a higher court for further investigation in the case.
The hearing in the case had concluded on July 3.
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The petition demanded that Modi and 59 others -- including senior police officers and bureaucrats -- be made accused for allegedly being part of a conspiracy which facilitated the riots.
Ehsan Jafri, a Congress leader, was among 68 people who were killed at the Gulberg Society here when a mob attacked it on February 28, 2002, a day after the Godhra train burning incident which set off riots in the state.
In December 2013, a metropolitan court had rejected Jafri's plea to book Modi and others for criminal conspiracy, after which she moved the high court in 2014.
The SIT had on February 8, 2012 filed a closure report and given clean chit to Modi and others in the case.
The lower court looked into all aspects of allegations to conclude that there was no further need to investigate the matter from the angle of "larger conspiracy", the SIT argued.
Jafri's lawyer Mihir Desai earlier argued in the HC that the magistrate, while accepting the SIT's closure report, did not even consider other options such as rejecting the report or ordering a fresh probe.
The lower court ignored the Supreme Court's guidelines and did not consider the signed statements of witnesses which suggested that there was a conspiracy, he had argued.
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