On January 3, 2015, the 21st Amendment Bill was tabled inside the National Assembly. It was expected the amendment would pass quickly without any opposition. The consensus among political leadership of country had already been achieved during a marathon 16-hour meeting on December 24, 2014.

One exception was Maulana Fazalur Rehman, chief of JUI-F, who strongly opposed the military courts on January 5, 2015, first during a press conference and then on the floor of the National Assembly.

Rehman said the government had not consulted his party while drafting the bill, despite being an ally. He objected to some passages of the bill, citing groups "using religion and a sect" while describing terrorists. He claimed the wording was discriminatory against religious groups and madrassas.

Jamaat-i-Islami (JI) also supported Rehman’s argument. Both the parties abstained from voting.

Participants of the meetings, who do not want to be identified, say Maulana had raised some objections which were addressed by both the civil and the military leadership during the meetings. "The JUI-F leadership wanted to meet the army chief and the ISI head but the military leadership did not show willingness for holding such a meeting."

Both the JUI-F and JI have maintained strong links with the military establishment as major stakeholders in the Afghanistan and Kashmir policies of Pakistan during the last three decades or so. Their opposition to military’s demand is unusual. In the past, both parties have supported the military establishment several times and vice versa.

In 2003, both the parties (as MMA) voted for the 17th amendment, which incorporated the Legal Framework Order into the constitution and provided a safe passage to the dictatorship of General Musharraf. It is believed that both the parties did so in a bid to return the favour which the establishment had given them in the shape of an electoral win in Balochistan and NWFP (now KP province) in the 2002 general elections.

It seems the relationship between JUI-F and the military establishment has not been at its best during the last few years. The party also refused to be part of Difa-e-Pakistan Council, an umbrella of 36 organisations, mainly religious, and people like General (retd) Hameed Gul -- formed in November 2011 in response to the deaths of 24 Pakistani soldiers who were killed by American planes along the Afghan border.

JUI-F believes the establishment is responsible for the rise of Imran Khan, which has marginalised JUI-F in KP. The relationship of the party with factions of TTP is also ambiguous. In June 2010, for instance, the JUI-F demanded the then government to release approximately 300 alleged Taliban members from prison, as they were also JUI-F party members. He used to term Taliban as "our boys".

After the 2008 general elections, it seems he fell out of favour with several TTP commanders. Ever since, many senior members of the party have been killed by the militants. Maulana Merajuddin, head of the JUI-F in Fata, was shot dead in May 2010. Rehman has himself survived three suicide bomb attacks.

To some, JUI-F not supporting military courts makes sense as madrassa and mosque are the basis of party’s religious activism and politics. Rehman and his party are also under immense pressure from the inside. The conservative religious vote bank has been drifting away from him.

During the 2008 elections, a splinter group of pro-Taliban leaders of JUI-F emerged in Balochistan. ASWJ has also been increasing its influence among the Deobandi youth. "Rehman tried to widen his support base among religious circles," says a senior member of ASWJ, another major Deobandi religious outfit which supports the idea of military courts.

"We supported the idea because the ground realities in Punjab are different. We want to save our workers," he says requesting anonymity, adding, "Rehman’s relations with the establishment are deteriorating."

Hafiz Hussain Ahmad, secretary information JUI-F, dispels the impression. "Our issue is not with the establishment but with the civilian government. The draft of the law was prepared by the civilian government and not the army," he clarifies.

He believes the government of Pakistan is increasing the pressure on religious parties and madrassas at the behest of America. "A majority of Afghan refugees in the 1980s got education in madrassas because the government did not build schools for them. None of them was trained at madrassas but at the camps run by the Pakistani government. Many of them joined the jihad in Afghanistan. They also used them in Kashmir and Afghanistan," he says.

The JUI-F is dubbed pro-establishment because it never resisted the imposition of martial law. Instead, it tried to provide a safe passage to military dictators. "We have not changed our position. It is up to ‘them’ to what extent they come closer to us," says Ahmad, replying to a question regarding JUI-F’s relationship with the military.

The JI, on the other hand, remained in the good books of military establishment since the early 1970s when its youth wing actively joined the civil war alongside Pakistani troops in 1971 fighting against nationalist Bengalis in Bangladesh (then East Pakistan).

The party was also a part of Difa-e-Pakistan. Its relationship with the establishment soured in Nov 2013 when the ISPR issued a press release in response to former JI chief Syed Munawar Hassan’s controversial statements in which he termed former TTP chief Hakeemullah Mehsud as a martyr and derided military personnel who had rendered sacrifices in the war against terrorists.

The election of Sirajul Haq as chief of JI is also being seen as a move to mend relations with the establishment. Experts believe JI’s opposition to military courts needs to be seen in the current scenario. "To me, JI’s opposition is in reaction to JUI-F as it cannot afford JUI-F taking advantage of the situation," says Hasan Khan, an Islamabad based journalist.

"There is a difference between the reaction of JI and JUI-F. JI has no plans to agitate against military courts but JUI-F is reportedly preparing to start agitation against military courts," he says. "JI has also been making efforts to shed its image as establishment’s B team. But it is not easy, as both the establishment and JI have similar slogans and narrative."

Experts on security issues say the current divide between the military establishment and religious parties may be permanent. "They are no more assets but have become stakeholders. I do not see a convergence of interests between the establishment and religious parties in the near future. The establishment will have to find new allies among secular parties, like MQM or may be PPP," says Amir Rana, an expert on counterterrorism and a member of the committee that formed national action plan against terrorism. "The military establishment has not always sided with religious parties. I think people need to recall Ayub Khan’s era as well."

Former ISI chief, General (retd) Hameed Gul, however, thinks otherwise. "Religious circles have suspected that military courts are being established to punish them."

"The takfiri lot of young Muslim jihadis can only be countered with a counter-narrative. They will only listen to the maulvi and if you push the maulvi to the wall, it would create more problems," he warns.