All the five cases were clubbed by the lower court for the purpose of framing of charges and trial.
The accused facing trial in the case are Mohd Shakeel, Mohd Saif, Zeeshan Ahmed, Zia-ur-Rehaman, Saquib Nisar, Mohd Sadique, Kayamuddin Kapadia, Mohd Hakim, Mohd Mansoor Ashgar Peerbhoy, Mubin Kadar Sheikh, Asif Bashiruddin, Mohd Akbar Ismail Chaudhary and Shahzad Ahmed.
According to NIA, Bhatkal, wanted in around 40 terror cases and carrying a reward of Rs 35 lakh, and Akhtar were arrested from the Indo-Nepal border on the night of August 28.
Since their arrest, both the accused are in custody of NIA and Delhi Police in connection with various terror cases.
Bhatkal, who hails from Bhatkal village in Udupi district of north Karnataka, was allegedly involved in a string of terror attacks in Ahmedabad, Surat, Bangalore, Pune, Delhi and Hyderabad, NIA had said.
30-year-old Bhatkal, who was earlier associated with banned outfit Students Islamic Movement of India (SIMI), is suspected to have hatched a conspiracy with others to wage war against India.