As America approaches a historic transfer of power, it is becoming ever-clearer what a daunting set of tasks awaits the new administration. When Barack Obama takes the oath of office at noon on January 20 he will inherit an economy collapsing before our eyes and a pair of ongoing wars in Afghanistan and Iraq. But he will also inherit a federal government whose machinery should bear an “out of order” sign.

Today’s dedication of the George W. Bush Presidential Library and Museum will bring together all of America’s living ex-presidents for what will likely be a warm and celebratory event. Protocol for the unveiling of presidential portraits and presidential libraries general calls for an abundance of courtesy and good feelings, with politics to be left at the front door.

Like all presidential libraries, this one — built on the campus of Southern Methodist University in Dallas — largely reflects the president’s own view of his time in office. The library and museum also reflects the 43rd president’s unique demeanor — “straightforward, confident, unapologetic and willing to let history be the ultimate decider of his time in office,” according to the Washington Post.

But there are other views, of course. George W. Bush’s presidency — like most — was also marked by controversy, tragedy, bitter political rancor and failings large and small. As the Bush administration ended in Dec. 2008, the Center for Public Integrity took stock of what went wrong during those years in its Broken Government project. In a comprehensive assessment of systematic failures over the previous eight years, the Center found more than 125 examples of government breakdown.

Read the project: Broken Government

The fine particle pollution that blasts into the air from diesel vehicles and power plants is a health threat well-understood by scientists — causing an estimated 20,000 deaths a year and hospitalizing many more in the United States. But faced with this issue, the Environmental Protection Agency (EPA) for the first time in three decades ignored the advice of its Clean Air Scientific Advisory Committee (CASAC) on air quality standards. Agency administrator Stephen L. Johnson said his 2006 ruling on National Ambient Air Quality Standards for fine particulate matter was “based on the best available science,” as required by the Clean Air Act. But it wasn’t clear what science he was referring to. The CASAC’s disagreements with the parent agency were echoed by the American Medical Association, American Thoracic Society, American Lung Association, American Academy of Pediatrics, American Heart Association, American Cancer Society, and American Public Health Association. EPA did issue a rule requiring that daily exposure levels to fine particulate matter be cut nearly in half by single or multi-county “areas,” to fit just within the revised window recommended by CASAC. But when the committee also recommended toughening the annual air standard for fine particulate matter, EPA disregarded the request.

Critics believe a lack of government regulation helped fuel questionable accounting practices — practices that allowed the huge energy trading firm Enron to report profits of hundreds of millions of dollars ($979 million in 2000, alone) before collapsing in 2001, in what was then the largest corporate bankruptcy in U.S. history. The erosion of accounting practices was believed to have begun in the 1980s, as firms tried to balance strict standards with a desire to please clients and expand consulting business, but the scandals burst into public view under President George W. Bush. Certainly by the time Bush was elected, there was ample reason to question the overall validity of corporate financial statements, given that restatements of Securities and Exchange Commission (SEC) filings had skyrocketed from just three in 1981 to 270 in 2001. (The SEC says some of the blame lies with the Financial Accounting Standards Board, the private nonprofit organization it designated to set rules for corporate financial disclosure. In 2000, for example, it adopted a rule allowing companies, including Enron, to keep certain holdings off their balance sheets.)

In October 2008, a draft intelligence assessment found that, despite the seven-year presence of U.S. troops, Afghanistan is in a “downward spiral” as the Taliban renews its influence over the country it once controlled. The draft National Intelligence Estimate, a formal document that reflects the consensus judgments of all 16 American intelligence agencies, faults the Afghan central government for the deteriorating situation, including rampant government corruption, as well as the country’s booming and destabilizing heroin trade. The New York Times reported that the assessment’s “conclusions represent a harsh verdict on decision-making in the Bush administration, which in the months after the September 11, 2001, attacks made Afghanistan the central focus of a global campaign against terrorism.” Critics have long said that the war in Iraq has distracted from the “forgotten war” in Afghanistan and that a lack of troops has hampered attempts to fully secure the country. Furthermore, the Taliban has established the border area in Pakistan’s Federally Administered Tribal Areas as a base for incursions into Afghanistan. The Pakistani government has weak control over these areas and violence in Afghanistan has increased markedly, starting in 2005. A U.S. effort to encourage the Pakistani government to control Taliban and Al Qaeda militants has failed to end the safe haven.