Ehsan Jafri, Zakia's husband and former Congress MP, was one of those who were slain during the riots across Gujarat after the Godhra incident.
Advocate Sanjay Parikh, Jafri's lawyer, made the allegation during the argument before Metropolitan Magistrate B J Ganatra.
The court is hearing Jafri's petition against closure report of Special Investigation Team which gave a clean chit to Modi and others in the face of the charge of complicity in the riots as levelled by Jafri in her complaint in 2008 before the Supreme Court.
"After the Godhra train burning incident, a large number of kar sevaks indulged in provocative slogan-shouting at Godhra railway station and the situation was tense...And what he (Modi) did was to call VHP Gujarat general secretary Jaideep Patel to go to Godhra and Patel instigated other VHP men and Hindus against Muslims. Therefore, Modi conspired with Jaideep Patel to instigate negative and aggressive feelings of RSS, VHP workers against Muslims," advocate Parikh contended.
"Real conspiracy began with this instruction to Patel. He (Modi) is the chief executor of the conspiracy," Parikh said, adding SIT failed to probe this aspect of the case.
Jaideep Patel, with 81 others, is facing trial in Naroda Gaam case in which 11 people from the minority community were killed.
Jafri's `protest petition' demands rejection of SIT report and seeks further investigation by an independent agency. Her complaint accuses Modi of being involved in the conspiracy behind wide-spread violence and misuse of the state machinery during the riots.