After the Sikh resistance had been overcome, only a few snipers remained. Following the execution of pilgrims, immediately after the main battle, those that survived were rounded up, detained by the Army and charged as terrorists:
“379 of the alleged ‘most dangerous terrorists’ were forced to sign a common confessional statement and thereafter served a common charge sheet that they were all Bhindranwale’s closest associates and comrades-in-arms engaged in ‘waging war against the State’. They were, therefore, detained under the NSA and are now being tried at Jodhpur under the Terrorist-Affected Areas (Special Courts) Act of 1984. As we were curious regarding the extent of danger these hardcore ‘terrorists’ posed to the State ‘with the intention to establish a State independent from the Government of India to be known as Khalistan”, we visited the homes of some of the Jodhpur detainees and met their families or relatives.
The evidence collected established beyond doubt that none of the Jodhpur detainees we succeeded in profiling are ‘terrorists’ but rather all of them are completely innocent, ordinary persons, whose only crime was that they had all gone to or were coming from the Golden Temple as devotees or pilgrims visiting the Golden Temple for the Guru Purab on June 3, 1984 or farmers gone to the Temple to deliver village donations of grain to the S.G.P.C. or students gone to pay obeisance at their holiest religious shrine, the Harmandir Sahib.”
Source; Citizens for Democracy; Report to the Nation: Oppression in Punjab (Bombay, 1985). via NSYF
These detainees were detained for up to 5 years, before in the face of worldwide condemnation and protest they were finally released.