In December 1997, an Egyptian agent who had been vetted and polygraphed by his CIA handlers collected a soil sample 60 feet in front of the entrance to the El-Shifa pharmaceutical plant in Khartoum, Sudan, which the agency believed was connected to Osama bin Laden. The soil sample -- apparently taken from land not belonging to El-Shifa -- was analyzed and found to contain two-and-a-half times the normal trace of O-ethyl methylphosphonothioic acid, or Empta, a chemical precursor used in the production of VX nerve gas. Throughout 1998, intelligence analysts debated what to conclude from the soil sample, since it did not demonstrate whether the plant actually manufactured nerve gas. In July, the CIA recommended collecting an additional sample (that never happened), while on August 6, the State Department's Bureau of Intelligence and Research concluded that "the evidence linking El-Shifa to bin Laden and chemical weapons was weak." The following day, two truck bombs planted by al Qaeda cells killed 213 people -- including 12 Americans -- at the U.S. embassy in Nairobi, Kenya, and 11 more people outside the U.S. embassy in Dar es Salaam, Tanzania.
A small group of senior Clinton administration officials debated a military response, which included five targets in Khartoum nominated by the CIA. Eventually, those five were whittled down to two and then to one. On August 20, two U.S. Navy warships launched 13 cruise missiles -- extra missiles were added to assure all the toxins would be incinerated -- at El-Shifa, destroying it and killing its night watchman. When it quickly became apparent that bin Laden had no controlling interest in El-Shifa, Clinton administration officials settled on the single soil sample as being the strongest evidence to justify the attack. Six weeks later, President Clinton told historian Taylor Branch that the supporting intelligence included "soil samples, connecting an element in nerve gas found there and in Afghanistan at similarly high concentrations."