With Pakistan’s civilian government and judiciary showing renewed signs of life, it’s time for them to ask the question the country has been avoiding for nine months: How did Osama bin Laden, the world’s leading terrorist, hide out in a military garrison city near Islamabad without anyone knowing?

To ask this question is not to accuse the Pakistani military or intelligence service of wrongdoing. So far, no “smoking gun” has emerged. But many puzzling issues surround bin Laden’s stay in Abbottabad for six years. Nobody should want them answered more than Gen. Ashfaq Kayani, the chief of army staff, who would gain new credibility at home and abroad by allowing such a probe.

Gen. Mike Hayden, the former CIA director, sums up a feeling that’s widespread among both Americans and Pakistanis when he says: “Without being accusatory, I think it’s certainly in Pakistan’s interest to clear the air.”

Implausible as it may sound, U.S. officials say that they don’t have any evidence that Kayani or other top Pakistani officials knew of bin Laden’s presence before the May 2 raid that killed the al-Qaeda leader. This assessment is based on the review of materials taken from bin Laden’s compound, plus the reactions of Kayani and other officials the night of the raid.

What makes an investigation seem possible now is that the Pakistani government, often under the military’s thumb, has been asserting its independence. The parliament has been examining how to “reset” the U.S.-Pakistan relationship; the Supreme Court has indicted Prime Minister Yousuf Raza Gilani in a corruption scandal and, notably, has scolded the Inter-Services Intelligence directorate for its treatment of prisoners; and President Asif Ali Zardari has managed to stay in power despite perpetual rumors that the military wants him out.

To lead Pakistan out of its wilderness of mirrors, Chief Justice Iftikhar Mohammed Chaudhry should form a special commission to examine the loose ends of the bin Laden story. Based on conversations with U.S., Pakistani and other officials, here are some questions that deserve answers:

●How did bin Laden come to Abbottabad in 2005, and what did Pakistani officials know about his whereabouts? Kayani was ISI chief at that time, but the dominant figure was President Pervez Musharraf, the former army chief. The commander of the military academy at Abbottabad starting in 2006 was Lt. Gen. Nadeem Taj, who succeeded Kayani as head of the ISI in 2007.

●Who owned the compound in 2005, and how was it readied for the new guest? I’m told that the original property records have disappeared, so the answers here are murky. But one intelligence source tells me that the architect who worked on the compound was regularly employed by the ISI; the architect reportedly was told only that a “highly placed VIP” was coming.

●What about the recent claim by former general Ziauddin Butt, former chief of the ISI, that the Abbottabad safe house was used by the Intelligence Bureau, another Pakistani spy agency? According to a December report in the Pakistani press, Butt said that bin Laden’s stay at Abbottabad was arranged by Brig. Gen. Ijaz Shah, head of the bureau from 2004 to 2008, on Musharraf’s orders. A Pakistani journalist named Arif Jamal recently published an article describing Shah as bin Laden’s “handler.”

●Whom did bin Laden contact while he was at Abbottabad? Though materials taken from the compound don’t show direct links with top Pakistani officials, U.S. analysts have found evidence that the al-Qaeda chief communicated with Mohammad Omar, leader of the Taliban, and with the Kashmiri militant group Lashkar-i-Taiba. The ISI is thought to monitor both groups closely; how did the messages slip through the net?

●What about the rumor that bin Laden was suffering from kidney failure and required dialysis? This canard was repeated for years, notably by Musharraf. CIA analysts were always dubious, and no dialysis machines were found at Abbottabad. So was this a deliberate piece of misinformation? And what about bin Laden’s claim in November 2001 to Pakistani journalist Hamid Mir that he had nuclear and chemical weapons? Was that a Pakistan-facilitated attempt to promote what bin Laden called his “deterrent” against a U.S. reprisal attack?

The list of unanswered questions goes on. But this sampling is enough to raise anyone’s eyebrows. For Pakistan to step foursquare into the future, and put this dreadful decade of lies and suspicion behind, it’s time for an official inquiry — not to please America, but to ensure the dignity of Pakistan.