The Defense Department admits to having detained over 80,000 people in facilities from Afghanistan to Guantanamo since the 9/11 attacks. At least 14,500 people are currently in US custody in connection with the war on terror; around 13,814 are being held in Iraq and some 500 detainees are at the Guantanamo detention facility. An unknown number are being held in Afghanistan and elsewhere. The Bush administration has defended its incarceration of so many detainees, many without charge or legal representation, from criticism by human rights organizations, civil liberties groups, and political opponents. What many find indefensible is the CIA’s practice of “rendering” terror suspects to foreign countries for interrogation and torture, as well as making some prisoners “disappear” into secret prisons in foreign countries. Currently, the Bush administration is attempting to counter reports that the CIA has used private jets to transport suspects to at least six countries, either in Europe or through European countries’ airspace. “If these allegations turn out to be true, the crucial thing is whether these flights landed in the member states with or without the knowledge and approval of the authorities,” says Terry Davis, the Council of Europe’s secretary general. The CIA has refused to comment on this or other reports. [Guardian, 11/18/2005]
November 22, 2005: Padilla Indicted for Lesser Crimes, Not on ‘Dirty Bomb’ Allegations
Jose Padilla, a US citizen and “enemy combatant” alleged to be an al-Qaeda terrorist (see May 8, 2002) and held without charges for over three years (see October 9, 2005), is charged with being part of a North American terrorist cell that sent money and recruits overseas to, as the indictment reads, “murder, maim, and kidnap.” The indictment contains none of the sensational allegations that the US government has made against Padilla (see June 10, 2002), including his supposed plan to detonate a “dirty bomb” inside the US (see Early 2002) and his plans to blow up US hotel and apartment buildings (see March 2002). Nor does the indictment accuse Padilla of being a member of al-Qaeda. Attorney General Alberto Gonzales says, “The indictment alleges that Padilla traveled overseas to train as a terrorist (see September-October 2000) with the intention of fighting a violent jihad.” He refuses to say why the more serious charges were not filed. Some provisions of the Patriot Act helped the investigation, Gonzales adds: “By tearing down the artificial wall that would have prevented this kind of investigation in the past, we’re able to bring these terrorists to justice,” he says. The Padilla case has become a central part of the dispute over holding prisoners such as Padilla without charge; by charging Padilla with lesser crimes, the Bush administration avoids the possibility of the Supreme Court ruling that he and other “enemy combatants,” particularly American citizens, must either be tried or released. Law professor Eric Freedman says the Padilla indictment is an effort by the administration “to avoid an adverse decision of the Supreme Court.” Law professor Jenny Martinez, who represents Padilla, says: “There’s no guarantee the government won’t do this again to Mr. Padilla or others. The Supreme Court needs to review this case on the merits so the lower court decision is not left lying like a loaded gun for the government to use whenever it wants.” Padilla’s lawyers say the government’s case against their client is based on little more than “double and triple hearsay from secret witnesses, along with information allegedly obtained from Padilla himself during his two years of incommunicado interrogation.” Padilla will be transferred from military custody to the Justice Department, where he will await trial in a federal prison in Miami. He faces life in prison if convicted of conspiracy to murder, maim, and kidnap overseas. The lesser charges—providing material support to terrorists and conspiracy—carry maximum prison terms of 15 years each. [Associated Press, 11/22/2005; Fox News, 11/23/2005]
‘Dirty Bomb’ Allegations ‘Not Credible,’ Says Former FBI Agent – Retired FBI agent Jack Cloonan, an expert on al-Qaeda, later says: “The dirty bomb plot was simply not credible. The government would never have given up that case if there was any hint of credibility to it. Padilla didn’t stand trial for it, because there was no evidence to support it.” [Vanity Fair, 12/16/2008]
Issue with CIA Videotapes – In 2002, captured al-Qaeda leader Abu Zubaida identified Padilla as an al-Qaeda operative (see Mid-April 2002) and the government cited Zubaida as a source of information about Padilla after Padilla’s arrest. Yet, sometime this same month, the CIA destroys the videotapes of Zubaida’s interrogations from the time period where he allegedly identified Padilla (see November 2005). The Nation’s Aziz Huq will later comment: “Given the [Bush] administration’s reliance on Zubaida’s statements as evidence of Padilla’s guilt, tapes of Zubaida’s interrogation were clearly relevant to the Padilla trial.… A federal criminal statute prevents the destruction of any record for a foreseeable proceeding, even if the evidence is not admissible.… [I]t seems almost certain that preservation of the tapes was legally required by the Jose Padilla prosecution.” [Nation, 12/11/2007]
November 24, 2005: US Resumes Military Sales to Indonesia, Overriding Evidence Indonesian Military Killed US Citizens
The US lifts an arms embargo on Indonesia. The US imposed a limited arms ban in 1991 after the Indonesian military massacred civilians in East Timor. The arms ban was strengthened in 1999 after the Indonesian military committed more massacres as East Timor voted for independence. The Bush administration had long desired closer ties with the Indonesian military, but was held back by Congress, which imposed conditions before military relations could be reestablished. In particular, the Indonesian military was required to account for some atrocities, especially the alleged killing of several US teachers by Indonesian soldiers in the province of West Papua in 2002 (see August 31, 2002). Indonesia had yet to fulfill these conditions, but earlier in the month Congress inserted a loophole in the law, allowing the restrictions to be waived by the Bush administration if it was found necessary for national security reasons. The Bush administration uses the loophole during Thanksgiving vacation while Congress is out of session, despite the lack of any new national security reason to do so. The lifting of restrictions still falls short of full military relations the US has with most other countries in the region. The US also renewed training and educational exchanges with the Indonesian military earlier in the year. [International Herald Tribune, 11/24/2005] The killing of US teachers in Papua remains unresolved. In January 2006, the New York Times will report that Indonesian police have concluded that the Indonesian military committed the killings but are unwilling to officially report this because of diplomatic sensitivities between the US and Indonesia. [New York Times, 1/27/2006]
November 29, 2005: US Effort to Fight Terrorist Financing Has Been ‘Spotty,’ Plagued by Infighting and Neglect
A new report by the Government Accountability Office (GAO), an impartial investigative arm of Congress, claims the US effort to help foreign nations cut off terrorism funding has been frustrated by infighting among US agencies, a lack of funding, and leadership problems. The report says “the US government lacks an integrated strategy” to train foreign countries and give them technical assistance. Officials at the State and Treasury Departments cannot even agree on who is supposed to be in charge of the effort. In at least one case, the State Department refused to even allow a Treasury official to enter a certain foreign country. “Investigators found clear tensions between officials at State, Treasury, Justice, and other US government departments.” Remarkably, private contractors have sometimes been allowed to draft proposed laws for foreign countries to curb terrorist financing. The contractors’ work at times resulted in proposals with “substantial deficiencies.” Generally speaking, the New York Times notes that experts say that the Bush administration’s efforts with terrorist financing has been “spotty, with few clear dents in al-Qaeda’s ability to move money and finance terrorist attacks.” [New York Times, 11/29/2005]
Late 2005: Justice Department Issues Secret Ruling Declaring All CIA Interrogation Techniques Legal
As Congress debates legislation that will outlaw “cruel, inhuman, and degrading” treatment of terrorist suspects and detainees in US custody, the Justice Department issues a secret opinion, one that few lawmakers even know exists, ruling that none of the CIA’s interrogation methods violate that standard. The Justice Department has already issued one secret opinion countermanding the Bush administration’s stated position that torture is “abhorrent” (see February 2005). Both rulings are efforts by Attorney General Alberto Gonzales and White House officials to realign the Justice Department with the White House after an in-house revolt by many Justice officials threw administration policies on torture and domestic surveillance into doubt (see Late 2003-2005). Though the public debate on torture becomes ever more pervasive during President Bush’s second term, the two rulings will remain in effect through the end of 2007 and beyond, helping the White House give US officials the broadest possible legal latitude for abusing and torturing prisoners. As late as October 2007, the White House will insist that it has always followed US and international law in its authorization of interrogation practices. Those assurances will be countered by an array of current and former officials involved in counterterrorism (see October 3, 2007). [New York Times, 10/4/2007] In 2007, Jameel Jaffer of the American Civil Liberties Union (ACLU) will say in conjunction with a lawsuit filed against the Justice Department’s interrogation practices, “These torture memos should never have been written, and it is utterly unacceptable that the administration continues to suppress them while at the same time declaring publicly that it abhors torture. It is now obvious that senior administration officials worked in concert over a period of several years to evade and violate the laws that prohibit cruelty and torture. Some degree of accountability is long overdue.” The ACLU will also note that the administration had failed to disclose the existence of the two opinions in its court filings, a failure characterized by the administration as an accidental oversight. [Harper’s, 11/7/2007]
December 5, 2005: 9/11 Commission Issues Critical Report Card on Public Security Reforms, Then Disbands
The ten ex-9/11 Commissioners issue a report card to monitor the progress on implementation of the commission’s recommendations given in their July 2004 final report, and they generally give harsh grades. The report card assigns letter grades to the commission’s 41 key recommendations. In nearly half the categories, the government receives a D, F, or incomplete grade. There is only one high grade, an A-minus for its “vigorous effort against terrorist financing.” [Washington Post, 12/6/2005] Ironically, that one good grade runs counter to the opinion of many counterterrorism experts. For instance, author Zachary Abuza has said, “The glaring exception to the success in fighting terrorism has been on the financial front…” [Contemporary Southeast Asia, 8/1/2003] The report card criticizes the government for: 
still not checking the identities of airplane passengers against a complete terrorism watch list. continuing to allocate domestic security funding without considering that certain parts of the country are at greater risk than others. excessive secrecy regarding intelligence spending. the handling of detainees. persistent problems in first responder communication systems. [Los Angeles Times, 12/5/2005] the slow transformation of and continuing problems with the FBI. [Washington Post, 12/6/2005]
The report does not give grades to President Bush or any other specific officials. The 9/11 Commission formally ceased operations after issuing its final report, but some members formed a privately funded foundation to monitor progress. The foundation disbands after releasing the report card. White House spokesman Scott McClellan defends the Bush administration’s efforts, saying, “The best way to protect the American people is to take the fight to the enemy, to stay on the offensive.” [Los Angeles Times, 12/5/2005]
May 2006: FEMA Warns of Nuclear ‘Suitcase Bombs’
The Federal Emergency Management Agency posts a warning from the White House on its Web site about “dirty bombs” and radiological “suitcase bombs.” The warning says that a terrorist’s nuclear weapon would “probably be limited to a single smaller ‘suitcase’ weapon.” It adds: “The strength of such a weapon would be in the range of the bombs used during World War II. The nature of the effects would be the same as a weapon delivered by an intercontinental missile, but the area and severity of the effects would be significantly more limited.” [Federal Emergency Management Agency, 5/2006] In late 2007, a senior FBI agent will say that such “suitcase nukes” are unlikely to exist outside of fiction (see November 10, 2007).
May 4, 2006: Former US Intelligence Official Says Bush Administration’s Prewar Allegations Were Part of an ‘Organized Campaign of Manipulation’
In an interview with the Spanish newspaper El Pais, former CIA senior analyst Paul Pillar says the Bush administration’s prewar allegations concerning Iraq were part of an “organized campaign of manipulation.” This was especially the case with the administration’s claims that Iraq was working with al-Qaeda, he says. “It was this that most strongly affected public opinion in the United States, and which would keep alive the images of September 11, 2001. The administration’s voracious appetite to obtain material about this non-existent alliance cost a great deal of time and work to senior intelligence staff and the most highly experienced analysts in the CIA.” Pillars also tells the newspaper the decision to invade Iraq was made “for other reasons and did not depend on weapons of mass destruction or the results of United Nations inspections.” [Agence France-Presse, 5/4/2006; El Pais, 5/4/2006]
May 5, 2006: CIA Director Goss Resigns amid Scandal; Replaced by Former NSA Director Michael Hayden
CIA Director Porter Goss abruptly resigns “amid allegations that he and a top aide may have attended Watergate poker parties where bribes and prostitutes were provided to a corrupt congressman.” A senior law enforcement official says, “It’s all about the Duke Cunningham scandal.” Congressman Randall “Duke” Cunningham (R-CA) was sentenced to eight years in prison after pleading guilty in late 2005 to taking millions of dollars in bribes. Goss is replaced by General Michael Hayden, the former director of the NSA. [New York Daily News, 5/6/2006] The Bush administration gives no explanation for the resignation and even Goss publicly describes his own resignation as “just one of those mysteries.” [CNN, 5/6/2006] It is later learned that Goss’s resignation is spurred in part because of the controversy surrounding his chosen CIA Executive Director, Kyle “Dusty” Foggo. Foggo is being investigated for his connections to Cunningham. Both Foggo and Cunningham are being investigated by the office of US Attorney Carol Lam (see November 8, 2002). [Talking Points Memo, 2011] In 2007, former senior CIA analyst Valerie Plame Wilson will write: “Once John Negroponte became the de facto intelligence czar as director of national intelligence (DNI—see February 17, 2005)… Goss’s effectiveness, prestige, and daily access to the president had been considerably diminished. This, in turn, further degraded and undermined the organization he led. During a time of driving massive change, which Goss and other senior intelligence managers were attempting to do at the agency, effective and clear communication with all levels of the organization is critical. Goss failed completely at this task and the cost was high.… [H]e had been a poor fit from the beginning. In an underperforming bureaucracy such as the CIA, a strong leader, respected by the rank and file, is essential to managing needed change and modernization. On a personal note, I was not sorry to see him go.” [Wilson, 2007, pp. 247-248]
June 30, 2006: Supreme Court Rules Existing Guantanamo Military Commissions Are Illegal; Detainees There Have Legal Rights
In the Hamdan v. Rumsfeld case, the Supreme Court rules 5-3 to strike down the Bush administration’s plans to try Guantanamo detainees before military commissions. Ruling in favor of detainee Salim Ahmed Hamdan (see November 8, 2004), the Court rules that the commissions are unauthorized by federal statutes and violate international law. Writing for the majority, Justice John Paul Stevens says, “The executive is bound to comply with the rule of law that prevails in this jurisdiction.” The opinion throws out each of the administration’s arguments in favor of the commissions, including its assertion that Congress had stripped the Supreme Court of the jurisdiction to decide the case. One of the major flaws in the commissions, the Court rules, is that President Bush unilaterally established them without the authorization of Congress. [New York Times, 6/30/2006] During the oral arguments three months before, Hamdan’s lawyer, Neal Katyal, told the Court: “The whole point of this [proceeding] is to say we’re challenging the lawfulness of the tribunal [the military commissions] itself. This isn’t a challenge to some decision that a court makes. This is a challenge to the court itself, and that’s why it’s different than the ordinary criminal context that you’re positing.” [Savage, 2007, pp. 274-275]
Major Defeat for Bush Administration – Civil libertarian and human rights organizations consider the ruling a shattering defeat for the administration, particularly in its assertions of expansive, unfettered presidential authority. Bush says in light of the decision, he will work with Congress to “find a way forward” to implement the commissions. “The ruling destroys one of the key pillars of the Guantanamo system,” says Gerald Staberock, a director of the International Commission of Jurists. “Guantanamo was built on the idea that prisoners there have limited rights. There is no longer that legal black hole.” The ruling also says that prisoners held as “enemy combatants” must be afforded rights under the Geneva Conventions, specifically those requiring humane treatment for detainees and the right to free and open trials in the US legal system. While some form of military trials may be permissible, the ruling states that defendants must be given basic rights such as the ability to attend the trial and the right to see and challenge evidence submitted by the prosecution. Stevens writes that the historical origin of military commissions was in their use as a “tribunal of necessity” under wartime conditions. “Exigency lent the commission its legitimacy, but did not further justify the wholesale jettisoning of procedural protections.” [New York Times, 6/30/2006] In 2007, author and reporter Charlie Savage will write, “Five justices on the Supreme Court said Bush had broken the law.” [Savage, 2007, pp. 275]
Hardline Conservative Justices Dissent – Stevens is joined by Justices David Souter, Stephen Breyer, and Ruth Bader Ginsburg. Justice Anthony Kennedy issues a concurring opinion. Dissenting are Justices Samuel Alito, Antonin Scalia, and Clarence Thomas. Thomas, in a dissent signed by Scalia and Alito, calls the decision “untenable” and “dangerous.” Chief Justice John Roberts recused himself from the case because of his participation in a federal appeals court that ruled in favor of the administration (see November 8, 2004).
Not Charged for Three Years – Hamdan is a Guantanamo detainee from Yemen, captured in Afghanistan in November 2001 and taken to Guantanamo in June 2002. He is accused of being a member of al-Qaeda, in his function as driver and bodyguard for Osama bin Laden. He was not charged with a crime—conspiracy—until mid-2004. [New York Times, 6/30/2006]
