Md. Shahid and Md. Rashid were arrested in December by Delhi Police from Haryana's Mewat district.
Their counsel M.S. Khan has sought transfer of the case from Delhi Police to the National Investigation Agency (NIA) for a fair probe into the matter, contending that his clients were made scapegoats.
"Rahul Gandhi made a revelation during his public meeting in Indore Oct 24, 2013 that an officer of the Intelligence Bureau briefed him about the infiltration of ISI in relief camps in Muzaffarnagar for the purpose of recruitment of youngsters. He further revealed that the said officer also contacted those youngsters," Khan said in his letter to Home Minister Sushilkumar Shinde.
He said that on the basis of the alleged secret input received from the intelligence agency, "those two people have been connected in such a manner so as to prove the contents of the speech of Rahul Gandhi as true".
Delhi Police, on the basis of inputs by an intelligence agency, registered in December a case of criminal conspiracy and membership of the banned terrorist outfit.
Acting on the information, Shahid and Rashid were arrested.
Delhi Police sources earlier said Shahid and Rashid with another LeT member went to collect scriptures from Muzaffarnagar to radicalise the riot victims to join the outfit.
Counsel Khan said there were several loopholes in the story projected by police, but those cannnot be disclosed as it would destroy the defence of the accused.
Khan requested the home ministry to direct the NIA to investigate his clients' case in a fair and impartial manner, saying that the matter has national ramifications.
On March 28, 2013, the home ministry issued a notification facilitating the NIA to take over the case after the arrest of Liaqat, a 58-year-old resident of Muzaffarnagar and a government school teacher, generated conflicting versions from Delhi and Jammu and Kashmir Police.