The first signs of political ferment against Islamabad appeared in 1971 when an organisation called the Tanzeem-e-Millat (TM) started operating in Gilgit despite the ban on political activities. In 1974, Johar Ali Khan, the founder of the party, called for a strike to demand the repeal of the Frontier Crime Regulations (FCRs) and the recognition of the basic rights of the locals. When the agitation took a violent turn, A.R.Siddiqui, the then Deputy Commissioner, ordered the Gilgit Scouts, a para-military unit raised by the British and with a history of over a hundred years, to fire on the agitators and disperse them. They refused to open fire on fellow-Shias. He then grabbed a rifle from a soldier of the Gilgit Scouts and opened fire on the crowd himself. One agitator was killed and the crowd dispersed Johar Ali Khan and 15 others were arrested and taken to the jail. A large number of Shias raided the jail and got them freed. They were subsequently re-arrested.
Following these violent incidents--the first in the history of the NA since the Pakistan Army occupied it-- Zulfiquar Ali Bhutto, then in power in Islamabad, issued a notification disbanding the Gilgit Scouts as a punishment for its refusing to fire on the Shia agitators. The disbanding of the unit hurt the feelings of the Shias. It also threw a large number, who served in the Scouts, out of job. This marked the beginning of the alienation of the Shias of the NA against Islamabad. Tracing the history of the alienation of the Shias of the NA, the Friday Times, a weekly of Lahore, wrote in its issue of October 15-21,1992, as follows: "The Gilgit Scouts was the only credible law-enforcing agency from pre-Partition times. Northerners generally resent the undoing of this centuries-old institution."
The widespread anger caused by the disbanding of the Gilgit Scouts led to the emergence of a number of anti-Government religious organisations of the Shias. To counter this, the local Army authorities allegedly encouraged the formation of pro-Government organisations by the Sunnis. This injected the poison of religious sectarianism in the NA, which like the rest of Jammu & Kashmir, had historically remained a tolerant society.
The injection of this poison led to an anti-Shia carnage in Gilgit in May 1988. This was followed by more anti-Shia incidents in 1990, 1992 and 1993. In its issue of April 1990, the Herald, the monthly journal of the Dawn group of publications of Karachi, wrote as follows: