Besides Haider, the court framed charges against Taufqiue Ansari and Mujibullah under Indian Penal Code, Explosive Substances Act and Unlawful Activities Prevention Act.
The trio have earlier been chargesheeted for their alleged involvement in serial blasts at 'Hunkar' rally in Patna in October last year which was addressed by the then BJP's Prime Ministerial candidate Narendra Modi.
NIA, which had earlier filed a charge sheet against the three accused on September 11 this year, had used various scientific methods to solve the serial bombings in the holy city on July seven last year that left five people injured.
Ali was linked to the case after NIA recovered a hair from a monk robe. After the DNA of the hair strand, his involvement in the case was made out.
The accused is alleged to have worn a monk's robe while planting the bomb.
NIA claimed the bombing was  done by Ali and others to avenge the the alleged atrocities on Rohingya Muslims in Buddist-majority Myanmar.
Ali and his associates were members of banned SIMI terror organisation who had been motivating and recruiting young boys from Ranchi and other places by way of lectures and showing Jihadi videos related to alleged atrocities on Muslims across the world including on Rohingya Muslims in Myanmar.
"In pursuance to this conspiracy, accused Haider Ali and his associates undertook five reconnaissance trips to Bodh Gaya to observe the security arrangements and decide the exact places where bombs were to be planted," NIA said in its chargesheet.
The accused procured material from different places and prepared cylinder bombs and executed the serial blasts. The scientific investigation, which included forensic analysis and DNA finger printing, had "established" the involvement of the arrested persons in the case, the agency said.

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