The Al-Shifa (الشفاء, Arabic for "healing") pharmaceutical factory in Khartoum North, Sudan was constructed between 1992 and 1996 with components imported from the United States, Sweden, Italy, Switzerland, Germany, India, and Thailand.
The industrial complex was composed of around four buildings. It was the largest pharmaceutical factory in Khartoum and employed over 300 workers, producing medicine both for human and veterinary use. The factory was used primarily for the manufacture of anti-malaria medicines and veterinary products.
The factory was destroyed in 1998 by a missile attack launched by the United States government, killing one employee and wounding eleven. Critics of the attack have estimated that up to tens of thousands of Sudanese civilians died throughout Sudan as the supply of necessary drugs was cut off. The US government stated several reasons for its attack:
These justifications for the bombing were disputed by the owners of the plant, the Sudanese government, and other governments.
On August 20, 1998, the factory was destroyed in cruise missile strikes launched by the United States in retaliation for the August 7 truck bomb attacks on its embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya (see 1998 U.S. embassy bombings). The administration of President Bill Clinton justified the attacks, dubbed Operation Infinite Reach, on the grounds that the al-Shifa plant was involved with processing the deadly nerve agent VX, and had ties with the Islamist al-Qaeda group of Osama bin Laden, which was believed to be behind the embassy bombings and Operation Bojinka. The August 20 U.S. action also hit al-Qaeda camps in Afghanistan, to where bin Laden had moved following his May 1996 expulsion from Sudan.
The key piece of physical evidence linking the al-Shifa facility to production of chemical weapons was the discovery of EMPTA in a soil sample taken from the plant during a CIA clandestine operation. EMPTA, or O-Ethyl methylphosphonothioic acid, is classified as a Schedule 2B compound according to the Chemical Weapons Convention and is a VX precursor. Although several theoretical uses for EMPTA were postulated as well as several patented process using EMPTA, such as the manufacture of plastic, no known industrial uses of EMPTA were ever documented nor any products that contained EMPTA. It is, however, not banned by the Chemical Weapons Convention as originally claimed by the US government. Moreover, it does not necessarily follow from the presence of EMPTA near (but outside) the boundary of Al-Shifa that this was produced in the factory: EMPTA could have been "stored in or transported near al-Shifa, instead of being produced by it," according to a report by Michael Barletta.
Under-Secretary of State Thomas Pickering claimed to have sufficient evidence against Sudan, including contacts between officials at Al-Shifa plant and Iraqi chemical weapons experts, with the Iraq chemical weapons program the only one identified with using EMPTA for VX production. The National Democratic Alliance (NDA), a Sudanese opposition in Cairo led by Mubarak Al-Mahdi, also insisted that the plant was producing ingredients for chemical weapons. Former Clinton administration counter terrorism advisor Richard Clarke and former national security advisor Sandy Berger also noted the facilities alleged ties with the former Iraqi government. Clarke also cited Iraq's $199,000 contract with al Shifa for veterinary medicine under the UN's Oil for Food Program.
Officials later acknowledged, however, "that the evidence that prompted President Clinton to order the missile strike on the Shifa plant was not as solid as first portrayed. Indeed, officials later said that there was no proof that the plant had been manufacturing or storing nerve gas, as initially suspected by the Americans, or had been linked to Osama bin Laden, who was a resident of Khartoum in the 1980s."
However, a Clinton State Department official had stated that a money manager for Bin Laden had claimed that Bin Laden had, indeed, invested in Al Shifa. And that the Al Shifa manager even lived in the same Sudan house Bin Laden himself had previously lived in.
The U.S. State Department Bureau of Intelligence and Research wrote a report in 1999 questioning the attack on the factory, suggesting that the connection to bin Laden was not accurate; James Risen reported in the New York Times: "Now, the analysts renewed their doubts and told Assistant Secretary of State Phyllis Oakley that the C.I.A.'s evidence on which the attack was based was inadequate. Ms. Oakley asked them to double-check; perhaps there was some intelligence they had not yet seen. The answer came back quickly: There was no additional evidence. Ms. Oakley called a meeting of key aides and a consensus emerged: Contrary to what the Administration was saying, the case tying Al Shifa to Mr. bin Laden or to chemical weapons was weak." The Chairman of El Shifa Pharmaceutical Industries, who is critical of the Sudanese government, more recently told reporters, "I had inventories of every chemical and records of every employee's history. There were no such [nerve gas] chemicals being made here."
Nonetheless, Clinton's Secretary of Defense William Cohen testified to the 9/11 Commission in 2004, characterizing Al Shifa as a "WMD-related facility", which played a "chemical weapons role" such as to pose a risk that it, with the help of the Iraqi chemical weapons program connections he also testified to, might help Al Qaeda get chemical weapons technology.
Sudan has since invited the U.S. to conduct chemical tests at the site for evidence to support its claim that the plant might have been a chemical weapons factory; so far, the U.S. has refused the invitation to investigate. Nevertheless, the U.S. has refused to officially apologize for the attacks, suggesting that some privately still suspect that chemical weapons activity existed there.
The Khartoum attack was noted for its outstanding precision, as successive missiles all but leveled the Al-Shifa works with minimal damage to surrounding areas, although one person was killed and ten wounded in the attack.
Directly after the strike the Sudanese government demanded that the Security Council conduct an investigation of the site to determine if it had been used to produce chemical weapons or precursors. Such an investigation was from the start opposed by the US. Nor has USA ever let an independent laboratory analyze the sample allegedly containing EMPTA. Michael Barletta concludes that there is no evidence the al-Shifa factory was ever involved in production of chemical weapons, and it is known that many of the initial US allegations were wrong.
The UK Observer head-lined the story with "[T]he loss of this factory is a tragedy for the rural communities who need these medicines" quoting Tom Carnaffin, technical manager with "intimate knowledge" of the destroyed plant. 3 months later, a correspondent of the same paper, Patrick Wintour, elaborated that the plant "provided 50 percent of Sudan’s medicines, and its destruction has left the country with no supplies of choloroquine, the standard treatment for malaria." He continued that, despite this, the British Government (who publicly backed the U.S. attack) refused requests "to resupply chloroquine in emergency relief until such time as the Sudanese can rebuild their pharmaceutical production." The factory was a principal source of Sudan's anti-malaria and veterinary drugs according to the CBW Conventions Bulletin.
Germany's ambassador to Sudan from 1996 to 2000, Werner Daum, wrote an article in 2001 in which he called "several tens of thousands of deaths" of Sudanese civilians caused by a medicine shortage a "reasonable guess". The regional director of the Near East Foundation, who had field experience in the Sudan, wrote an article in the Boston Globe with the same estimate and said "without the lifesaving medicine [the destroyed facilities] produced ... tens of thousands of people - many of them children - have suffered and died from malaria, tuberculosis and other treatable diseases ... produced 90 percent of Sudan's major pharmaceutical products ... Sanctions against Sudan made it impossible to import adequate amounts of medicines required to cover the serious gaps left by the plant's destruction ... Millions must wonder how the International Court of Justice in The Hague will celebrate this anniversary". The Al-Shifa facility was "the only one producing TB drugs - for more than 100,000 patients, at about 1 British pound a month" and "the only factory making veterinary drugs in this vast, mostly pastoralist, country. It's speciality was drugs to kill the parasites which pass from herds to herders, one of Sudan's principle causes of infant mortality".
In "9-11", Noam Chomsky argued that the bombing of Al-Shifa was a horrendous crime committed by the United States Government that resulted in the deaths of several hundreds of thousands of Sudanese people from treatable diseases such as malaria and tuberculosis because they were deprived of medicines manufactured at the plant. "Insofar as such consequences ensued, we may compare the crime in Sudan to the assassination of Lumumba, which helped plunge the Congo into decades of slaughter, still continuing, or the overthrow of the democratic government of Guatemala in 1954, which led to 40 years of hideous atrocities; and all too many others like it."
The estimates of the death toll were disputed by Keith Windschuttle and by Leo Casey, who said the figures were "fabricated out of whole cloth". Windschuttle claimed that Daum "had done no research into the matter" and that "the reports of the Sudanese operations of the several Western aid agencies, including Oxfam, Médecins sans Frontières, and Norwegian People’s Aid, who have been operating in this region for decades, will not find any evidence of an unusual increase in the death toll at the time."
Human Rights Watch reported that the bombing had the unintended effect of stopping relief efforts aimed at supplying food to areas of Sudan gripped by famine caused by that country's ongoing civil war. Many of these agencies had been wholly or partially manned by Americans who subsequently evacuated the country out of fear of retaliation spurred by negative responses by the Sudanese government. A letter by that agency to President Clinton stated "many relief efforts have been postponed indefinitely, including a crucial one run by the U.S.-based International Rescue Committee where more than fifty southerners are dying daily". Mark Huband in the Financial Times wrote that the attack "shattered ... the expected benefits of a political shift at the heart of Sudan's Islamicist government" towards a "pragmatic engagement with the outside world".
Outspoken Clinton critic Christopher Hitchens wrote that the factory "could not have been folded like a tent and spirited away in a day or so. And the United States has diplomatic relations with Sudan. ... Well then, what was the hurry? ... There is really only one possible answer to that question. Clinton needed to look 'presidential' for a day."
The 9/11 Commission Report evaluated such so-called "Wag the Dog" theories (the strikes being motivated to deflect attention from domestic, political troubles), and found no reason to believe them, nor disbelieve the testimony and assertions of former President Clinton, former Vice President Gore, CIA Chief Tenet, nor former security advisors Berger and Clarke that the destruction of Al Shifa was still, as of 2004, a justifible national security target. Page 118
The U.S. Justice Department, under President George W. Bush, produced an alleged al-Qaeda defector as a witness on February 13, 2001, in its ongoing case against Osama Bin Laden. The witness, Jamal Ahmad al-Fadl, testified that Al Qaeda operatives he was involved with had been engaged in manufacturing chemical weapons in Khartoum, Sudan, around 1993 or 1994. Page 524
According to The Guardian, "The factory's owner, Salah Idris, vigorously denied that he or the factory had any link with such weapons or any terrorist group. He is now suing the US government for £35 million after hiring experts to show that the plant made only medicines. Despite growing support for Idris's case in the US and Britain, Washington refuses to retract any of its claims and is contesting the lawsuit."
The Sudanese government wants the plant preserved in its destroyed condition as a reminder of the American attack and also offered an open door to the U.S. for chemical testing at the site, however, the U.S. refused the invitation. Sudan has asked the U.S. for an apology for the attack but the U.S. has refused on the grounds it has not ruled out the possibility the plant had some connection to chemical weapons development. 
The bombing of the al-Shifa factory resurfaced in the news in April, 2006, due to the firing of former CIA analyst Mary O'Neil McCarthy. McCarthy was against the bombing of the factory in 1998, and had written a formal letter of protest to President Clinton. According to former CIA analyst Michael Scheuer, she had voiced doubts that the factory had ties to al Qaeda or was producing chemical weapons. The New York Times reported: "In the case of the Al Shifa pharmaceutical plant in Khartoum, Sudan, her concerns may have been well-founded. Sudanese officials and the plant's owner denied any connection to Al Qaeda. In the aftermath of the attack, the internal White House debate over whether the intelligence reports about the plant were accurate spilled into the press. Eventually, Clinton administration officials conceded that the hardest evidence used to justify striking the plant was a single soil sample that seemed to indicate the presence of a chemical used in making VX gas."
Thomas Joscelyn quotes Daniel Benjamin, a former NSC staffer: "The report of the 9/11 Commission notes that the National Security staff reviewed the intelligence in April 2000 and concluded that the CIA's assessment of its intelligence on bin Laden and al-Shifa had been valid; the memo to Clinton on this was cosigned by Richard Clarke and Mary McCarthy, the NSC senior director for intelligence programs, who opposed the bombing of al-Shifa in 1998. The report also notes that in their testimony before the commission, Al Gore, Sandy Berger, George Tenet, and Richard Clarke all stood by the decision to bomb al-Shifa." 
Former Secretary of Defense Cohen defended, in his testimony to the 9/11 Commission in 2004, along with other cited Clinton security cabinet members in their separate 9/11 Commission testimony, the decision to destroy Al Shifa.: "At the time, the intelligence community at the highest level repeatedly assured us that "it never gets better than this" in terms of confidence in an intelligence conclusion regarding a hard target. There was a good reason for this confidence, including multiple, reinforcing elements of information ranging from links that the organization that built the facility had both with Bin Laden and with the leadership of the Iraqi chemical weapons program; extraordinary security when the facility was constructed; physical evidence from the site; and other information from HUMINT and technical sources. Given what we knew regarding terrorists’ interest in acquiring and using chemical weapons against Americans, and given the intelligence assessment provided us regarding the al-Shifa facility, I continue to believe that destroying it was the right decision."Page 14