The Indian Mujahideen was a homegrown organisation held responsible for a series of bombings across Indian cities in the second half of the 2000s. Because its units operated as dispersed cells rather than as a single visible structure, investigating it was primarily a problem of connection: establishing that offences in different states, at different times, belonged to the same network.
That work sat at the intersection of investigation and intelligence, and depended on sustained cooperation between state police forces and central agencies. Published reporting credits Deven Bharti with a significant role in the Mumbai Police investigations that dismantled Indian Mujahideen modules during this period.
The organisational detail of how such networks are identified is not described here, and should not be.