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

Despite the passage of new laws designed to protect them, whistleblowers have found themselves largely unprotected during the Bush administration. Six years ago, the Public Company Accounting Reform and Investor Protection Act of 2002, also known as the Sarbanes-Oxley corporate governance act, was passed in response to the Enron and WorldCom scandals. Provisions in the law made it illegal for publicly-traded companies to retaliate against “any other office, employee, contractor, subcontractor, or agent” of a company for acting as a whistleblower. Despite these strong provisions, the Department of Labor has ruled in favor of whistleblowers who claimed to be retaliated against only 17 times out of 1,273 complaints that were filed between 2002 and September 2008. Of those, 841 cases were dismissed, many on the technicality that the whistleblowers work for subsidiaries of the companies, not the main companies themselves. The Labor Department has argued that the statute does not cover employees of those subsidiaries. Senator Patrick Leahy, a Vermont Democrat, and Senator Charles Grassley, an Iowa Republican, who together drafted the protections, counter that there is no basis for this reading of the law. It is not just corporate whistleblowers who are not receiving the protection they expect; federal whistleblowers also find themselves without cover. In June 2008 a coalition of 112 independent groups urged the Senate and House to pass a new bill increasing whistleblower protection for federal employees. This call came after only two of 53 whistleblowers who brought cases to the Merit System Protection Board during the first three months of 2008 were victorious.

The Bush administration has consistently drawn ire from the scientific community for its propensity to ignore, manipulate, and suppress science. From its earliest days, the administration demonstrated a lack of interest or, say critics, even disdain for science by allowing key scientific posts to go unfilled for over a year — including Food and Drug Administration (FDA) commissioner, National Institutes of Health director, and surgeon general. The FDA job took 20 months to fill, while the eventual surgeon general, Richard Carmona, ultimately accused the administration of political interference. In addition, a presidential science adviser was not chosen for nine months, and then was demoted in status from “assistant to the president” to “adviser.”

In the confusion that reigned on September 11, 2001, the U.S. military was never positioned to shoot down any of the hijacked planes and even sent fighters after one of the flights long after it had crashed into the World Trade Center. “The civilian and military defenders of the nation's airspace — FAA [the Federal Aviation Administration] and NORAD [the North American Aerospace Defense Command] — were unprepared for the attacks launched against them,” the 9/11 Commission concluded. “Given that lack of preparedness, they attempted and failed to improvise an effective homeland defense against an unprecedented challenge.” Despite statements by Bush administration officials that it was unimaginable that terrorists would use hijacked places as missiles to crash into planes, NORAD actually ran drills in preparation for that scenario – which proved ineffective. Confronted by an actual attack, Air Force officials “did not know where to go or what targets they were to intercept.” according to the Government Accountability Office (GAO). “And once the shootdown order was given, it was not communicated to the pilots,” The 9/11 Commission had to dig to uncover the extent of the U.S. air defense system’s failure, including issuing subpoenas to both the FAA and NORAD to learn the truth, which was at odds with agency officials’ statements. Some Commission members reportedly urged a criminal investigation; instead, the matter was turned over to the inspectors general of the Transportation and Defense departments to determine whether to make criminal referrals to the Department of Justice. The inspectors general found no evidence that officials were knowingly misleading.