One of them, Arshid Qureshi worked as a guest relations officer at the controversial preacher Dr Zakir Naik's Islamic Research Foundation. Rizwan Khan, the other accused, is a cleric.
Both were handed over to Mumbai Police by their Kerala counterparts.
Mumbai Crime Branch has already arrested Mohammed Haneef, a cleric from Kerala, in this case. The fourth accused, Abdul Rashid Abdulla, a teacher, is suspected to have joined the Middle-East terror organisation ISIS.
Abdul Khan, a local resident, had filed a case with Mumbai Police after his son Ashfaque left for an ISIS-controlled territory with his wife and son. He was allegedly in touch with the accused.
Qureshi was nabbed in a joint operation by Kerala Police and Maharashtra ATS from Navi Mumbai on July 21, following a complaint lodged in Kochi by the brother of a young woman who was suspected to have joined ISIS with her husband.
Khan was apprehended from his residence at Kalyan in neighbouring Thane district on July 22.
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The court had framed the charges for alleged offences of criminal conspiracy (section 120B of IPC) and under provisions of Unlawful Activities Prevention Act (UAPA).
According to the probe agency, Hassan and Shaikh had been frequently visiting the UAE in connection with job since 2008 and 2012 respectively, while Islam had gone to join them in the UAE in July, 2015.
Hassan was earlier allegedly affiliated to the Indian Mujahideen and later got inclined towards ISIS, it alleged.
The charge sheet filed by NIA had claimed that the accused persons, in connivance with other known and unknown associates, had hatched a criminal conspiracy to propagate ideology, recruit persons, raise funds and facilitate the travel of the recruited persons to Syria to join the ISIS and further its activities.
"The accused had formed a terrorist gang and acted as a frontal group of the ISIS and incited, motivated, invited and facilitated people of different nationalities to leave their respective countries and travel to Syria to join, support and further activities of the ISIS," it said.
"They had voluntarily advocated and professed to be the supporters and members of the ISIS and actively supported, invited support from others, propagated and promoted unlawful activities and terrorist activities of the ISIS by exhorting, inciting, luring and influencing others to become members of this organisation by disseminating incriminating contents including sharing comments, pages, videos, images, literature and openly endorsing, justifying and glorifying the terrorist acts of the ISIS," the NIA had claimed.
"They had also raised, collected and received funds in the UAE and transferred it to their associates in India, the Philippines and Tunisia to facilitate their travel to Syria to join ISIS," the agency said.
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