The agency filed the compliant in a special court here against Arshi Qureshi (47) alias Arshid, a resident of Thane who has been arrested by the agency, and Abdul Rashid Abdulla (30), hailing from Kasaragod in Kerala, who is absconding.
The National Investigation Agency (NIA) said it has charged the two for "their involvement in unlawful activities and in spreading hatred against India and for providing support to the proscribed terrorist organisation ISIS by furthering its activities", under various sections of the Unlawful Activity (Prevention) Act.
"The case relates to the indoctrination of complainant's son Ashfak Majeed and his associates into extreme jihadi ideology by a group of like-minded youths from Kasaragod district of Kerala and some members of the Islamic Research Foundation (IRF) Mumbai who motivated and radicalised Ashfak and his associates to join the ISIS.
"Investigation by the NIA has established that Qureshi was involved in unlawful activities and in spreading hatred against India and was furthering the activities of the ISIS," it said.
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Wanted accused Abdulla, it added, was the main conspirator behind the offence of "motivating Ashfak and a number of other youths from Kasargod and Pallakkad districts of Kerala to join ISIS".
Taking cognisance of the case, the court fixed the next of hearing in the case on February 17.
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According to NIA, Ashfak's father said after his son met Qureshi in Mumbai, he changed and became more radical. He started following Islam in "orthodox and extremely conservative" manner.
Abdullah talked against democracy and expressed support for the attack on the office of French satirical magazine 'Charlie Hebdo', the NIA said.
"At this farm, the group used to read religious books, offer prayers, discuss topics like views on Islamic world, views on ISIS ideology, etc. They used to discuss that India is not a Dar-ul-Islam (land where Sharia is established) and India is a land of kafirs," said the charge sheet.
One of the missing youths, Bestin, was from a Catholic family and worked with an IBM call centre, the NIA said.
"He used to tell them (the youths who went missing) that Hijrat is duty of every Muslim. The Prophet had also shifted from Mecca to Medina so you should also change and leave your home. These teachings influenced the youngsters to leave their homes and join ISIS," the charge sheet said.