Editor’s note: As a result of errors, an earlier version of this column misrepresented quoted material. The corrected version is below.

The conviction of the Pakistani neuroscientist Aafia Siddiqui in New York last week of trying to kill American military officers and FBI agents illustrates that the greatest danger to our security comes not from al-Qaida but the thousands of shadowy mercenaries, kidnappers, killers and torturers our government employs around the globe.

The bizarre story surrounding Siddiqui, 37, who received an undergraduate degree from MIT and a doctorate in neuroscience from Brandeis University, often defies belief. Siddiqui, who could spend 50 years in prison on seven charges when she is sentenced in May, was by her own account abducted in 2003 from her hometown of Karachi, Pakistan, with her three children — two of whom remain missing — and spirited to a secret U.S. prison where she was allegedly tortured and mistreated for five years. The American government has no comment, either about the alleged clandestine detention or the missing children.

Siddiqui was discovered in 2008 disoriented and apparently aggressive and hostile, in Ghazni, Afghanistan, with her oldest son. She allegedly was carrying plans to make explosives, lists of New York landmarks and notes referring to “mass-casualty attacks.” But despite these claims the government prosecutors chose not to charge her with terrorism or links to al-Qaida — the reason for her original appearance on the FBI’s most-wanted list six years ago. Her supporters suggest that the papers she allegedly had in her possession when she was found in Afghanistan, rather than detail coherent plans for terrorist attacks, expose her severe mental deterioration, perhaps the result of years of imprisonment and abuse. This argument was bolstered by some of the pages of the documents shown briefly to the court, including a crude sketch of a gun that was described as a “match gun” that operates by lighting a match.

“Justice was not served,” Tina Foster, executive director of the International Justice Network and the spokesperson for Aafia Siddiqui’s family, told me. “The U.S. government made a decision to label this woman a terrorist, but instead of putting her on trial for the alleged terrorist activity she was put on trial for something else. They tried to convict her of that something else, not with evidence, but because she was a terrorist. She was selectively prosecuted for something that would allow them to only tell their side of the story.”

The government built its entire case instead around disputed events in the 300-square-foot room of the Ghazni police station. It insisted that on July 18, 2008, the diminutive Siddiqui, who had been arrested by local Afghan police the day before, seized an M4 assault rifle that was left unattended and fired at American military and FBI agents. None of the Americans were injured. Siddiqui, however, was gravely wounded, shot twice in the stomach.

No one, other than Siddiqui, has attempted to explain where she was for five years after she vanished in 2003. No one seems to be able to explain why a disoriented Pakistani woman and her son, an American citizen, neither of whom spoke Dari, were discovered by local residents wandering in a public square in Ghazni, where an eyewitness told Harpers Magazine the distraught Siddiqui “was attacking everyone who got close to her.” Had Siddiqui, after years of imprisonment and torture, perhaps been at the U.S. detention center in Bagram and then dumped with one of her three children in Ghazi? And where are the other two children, one of whom also is an American citizen? In an article written by Petra Bartosiewicz in the November 2009 Harper’s Magazine, authorities in Afghanistan described a series of events at odds with the official version.

The events of the following day are also subject to dispute. According to the complaint, a U.S. Army captain and a warrant officer, two FBI agents, and two military interpreters came to question Siddiqui at Ghazni’s police headquarters. The team was shown to a meeting room that was partitioned by a yellow curtain. “None of the United States personnel were aware,” the complaint states, “that Siddiqui was being held, unsecured, behind the curtain.” No explanation is offered as to why no one thought to look behind it. The group sat down to talk and, in another odd lapse of vigilance, “the Warrant Officer placed his United States Army M-4 rifle on the floor to his right next to the curtain, near his right foot.” Siddiqui, like a villain in a stage play, reached from behind the curtain and pulled the three-foot rifle to her side. She unlatched the safety. She pulled the curtain “slightly back” and pointed the gun directly at the head of the captain. One of the interpreters saw her. He lunged for the gun. Siddiqui shouted, “Get the fuck out of here!” and fired twice. She hit no one. As the interpreter wrestled her to the ground, the warrant officer drew his sidearm and fired “approximately two rounds” into Siddiqui’s abdomen. She collapsed, still struggling, then fell unconscious. The authorities in Afghanistan describe a different series of events. The governor of Ghazni Province, Usman Usmani, told my local reporter that the U.S. team had “demanded to take over custody” of Siddiqui. The governor refused. He could not release Siddiqui, he explained, until officials from the counterterrorism department in Kabul arrived to investigate. He proposed a compromise: the U.S. team could interview Siddiqui, but she would remain at the station. In a Reuters interview, however, a “senior Ghazni police officer” suggested that the compromise did not hold. The U.S. team arrived at the police station, he said, and demanded custody of Siddiqui, the Afghan officers refused, and the U.S. team proceeded to disarm them. Then, for reasons unexplained, Siddiqui herself somehow entered the scene. The U.S. team, “thinking that she had explosives and would attack them as a suicide bomber, shot her and took her.” Siddiqui’s own version of the shooting is less complicated. As she explained it to a delegation of Pakistani senators who came to Texas to visit her in prison a few months after her arrest, she never touched anyone’s gun, nor did she shout at anyone or make any threats. She simply stood up to see who was on the other side of the curtain and startled the soldiers. One of them shouted, “She is loose,” and then someone shot her. When she regained consciousness she heard someone else say, “We could lose our jobs.”

Siddiqui’s defense team pointed out that there was an absence of bullets, casings or residue from the M4, all of which suggested it had not been fired. They played a video to show that two holes in a wall supposedly caused by the M4 had been there before July 18. They also highlighted inconsistencies in the testimony from the nine government witnesses, who at times gave conflicting accounts of how many people were in the room, where they were sitting or standing and how many shots were fired.

Siddiqui, who took the stand during the trial against the advice of her defense team, called the report that she had fired the unattended M4 assault rifle at the Americans “the biggest lie.” She said she had been trying to flee the police station because she feared being tortured. Siddiqui, whose mental stability often appeared to be in question during the trial, was ejected several times from the Manhattan courtroom for erratic behavior and outbursts.

“It is difficult to get a fair trial in this country if the government wants to accuse you of terrorism,” said Foster. “It is difficult to get a fair trial on any types of charges. The government is allowed to tell the jury you are a terrorist before you have to put on any evidence. The fear factor that has emerged since 9/11 has permeated into the U.S. court system in a profoundly disturbing way. It embraces the idea that we can compromise core principles, for example the presumption of innocence, based on perceived threats that may or may not come to light. We, as a society, have chosen to cave on fear.”

I spent more than a year covering al-Qaida for The New York Times in Europe and the Middle East. The threat posed by Islamic extremists, while real, is also wildly overblown, used to foster a climate of fear and political passivity, as well as pump billions of dollars into the hands of the military, private contractors, intelligence agencies and repressive client governments including that of Pakistan. The leader of one FBI counterterrorism squad told The New York Times that of the 5,500 terrorism-related leads its 21 agents had pursued over the past five years, just 5 percent were credible and not one had foiled an actual terrorist plot. These statistics strike me as emblematic of the entire war on terror.

Terrorism, however, is a very good business. The number of extremists who are planning to carry out terrorist attacks is minuscule, but there are vast departments and legions of ambitious intelligence and military officers who desperately need to strike a tangible blow against terrorism, real or imagined, to promote their careers as well as justify obscene expenditures and a flagrant abuse of power. All this will not make us safer. It will not protect us from terrorist strikes. The more we dispatch brutal forms of power to the Islamic world the more enraged Muslims and terrorists we propel into the ranks of those who oppose us. The same perverted logic saw the Argentine military, when I lived in Buenos Aires, “disappear” 30,000 of the nation’s citizens, the vast majority of whom were innocent. Such logic also fed the drive to root out terrorists in El Salvador, where, when I arrived in 1983, the death squads were killing between 800 and 1,000 people a month. Once you build secret archipelagos of prisons, once you commit huge sums of money and invest your political capital in a ruthless war against subversion, once you empower a network of clandestine killers, operatives and torturers, you fuel the very insecurity and violence you seek to contain.

I do not know whether Siddiqui is innocent or guilty. But I do know that permitting jailers, spies, kidnappers and assassins to operate outside of the rule of law contaminates us with our own bile. Siddiqui is one victim. There are thousands more we do not see. These abuses, justified by the war on terror, have created a system of internal and external state terrorism that is far more dangerous to our security and democracy than the threat posed by Islamic radicals.