Mr. Haqqani is now under a Supreme Court investigation instigated by the country’s top generals. Mr. Haqqani denies writing the memo but has never made secret his distaste for the iron rule of Pakistan’s generals, who already felt humiliated by the surprise American raid on Osama bin Laden.

Mr. Haqqani’s passport has been confiscated, and he has taken refuge in Mr. Gilani’s home. The State Department has called for fair and transparent treatment of Mr. Haqqani in line with Pakistani and international law, and it must continue to press that point.

Two Pakistani officials and a journalist were assassinated last year — evidence of the country’s instability and a chilling warning to the few still brave enough to speak up for a tolerant and democratic society.

Pakistan’s Supreme Court is causing further trouble for the prime minister, threatening to remove him from office for failing to comply with court orders to reopen long-ago corruption cases against President Asif Ali Zardari, himself a fierce adversary of the military. According to a report in The Times, many Pakistani officials suspect the military is using the judiciary to weaken — even topple — the government before the March election for the Senate, which Mr. Zardari’s party is expected to win.

No civilian government in Pakistan has ever finished its term. This one has survived longer than the others and is up for re-election by 2013. Every effort must be made to have that vote go forward so another — and, one hopes, more competent — civilian government can succeed it. The court needs to stay out of politics and focus on building a fair, unbiased legal system. Likewise the military. The generals say they don’t want to govern, but no civilian will ever be able to do a competent job if the military keeps pulling the strings. Although relations with Pakistan are at an all-time low, the United States should keep engaging the country’s civilian leaders and encouraging its civil society whenever possible.