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Iftikhar Chaudhry, Pakistan's chief justice, is not short of chutzpah. In 2007 he was sacked as a troublemaker by General Pervez Musharraf, the former military dictator, after pursuing investigations into suspected killings by the security forces. The movement for his reinstatement played a big part in bringing Musharraf down and restoring civilian government. But Chaudhry has also been at odds with the new administration — so much so that President Asif Ali Zardari's men have painted him as a stooge of the army.

Now the judiciary is taking on the military establishment as well. It may be because Chaudhry's court is sensitive to these slurs on its independence; it may be because it has genuinely come round to the view that the powers of the army need to be curbed. Either way, this development is to be applauded: as our special report this week argues, the army's belief in its impunity is one of the country's biggest problems.

The seeds of the army's excessive power lie in Pakistan's origins. Born out of India, and created through a bloody partition, the country has always feared being swallowed up by its bigger neighbour. As a result, it has had since inception an army that is too big for the country's size, greedy for resources and dangerously interventionist.

The army's perception of itself as the guarantor of national security has led it to abuse its position. For half of Pakistan's 64-year life, it has governed the country; for the other half, it has rigged elections, financed politicians it favoured and undermined those it didn't. Politicians who want to make peace with India are a particular target.

The army's power shapes Pakistani foreign policy, too. Soldiers are more focused than civilians on the military threat from India, and that fear has dangerously influenced the country's dealings abroad. Pakistan plays a double game in Afghanistan, where the Taliban are at once its enemies (because they are the enemies of its ally America) and its friends (because they are the enemies of its enemy India). And few doubt that the Pakistani army's intelligence wing, the Inter-Services Intelligence (ISI), has also been in cahoots with groups responsible for atrocities in India as well.

The Supreme Court's political role is another consequence of the way the army has distorted the country's political life. Long periods of military rule, when the courts were the civilians' only defence against the soldiers, boosted the relative power of the judiciary while weakening the politicians. This has been compounded by Chaudhry's determination to pursue corruption charges against Zardari. In a country as riddled with graft as Pakistan, it is hard to complain about a judge trying to ferret out wrongdoing. But since Zardari enjoys constitutional immunity, the practical effect of the judge's onslaught will be to tie up the rest of the government's term — unlikely to last until its natural conclusion next year — with constitutional haggling.

Right target

So it is a relief that the Supreme Court is now turning its fire on the armed forces as well. It is to hear three petitions relating to the conduct of the army and the ISI. One petition asks what has happened to 11 alleged terrorists taken into custody, where four apparently died. Another tackles the security forces' behaviour in a vicious counter-insurgency campaign in Balochistan. The third dates all the way back to 1990 and the ISI's role in rigging an election.

By themselves, these cases will do little to shift the balance of power from the army to the civilians. Nothing that Pakistanis are likely to hear will surprise them. However, each case does touch on a different aspect of the many ways in which the security services have abused their power over the past few decades.

Even the suggestion that soldiers accused of abuses might be brought to book would begin to erode the army's sense of impunity. It could also set the stage for Pakistan to begin to look at the much deeper problems relating to the army's exceptionally privileged role in public life.

Such an overhaul would involve changing the laws that remove much military activity from civilian jurisdiction and tackling its outsized role in the economy. The country needs to spend less of its money on soldiers and more on educating its people: with its literacy rate a shameful 58 per cent, Pakistan is below far poorer countries such as Haiti and Congo.

There is a huge amount to set right. But the move by the judiciary against the army could at least start to make Pakistan's army accountable, if not to the political process, than at least to the law.