The Washington Post's "Top Secret America" series investigates the U.S. national security and intelligence system that is "so big, so complex and so hard to manage, no one really knows if it's fulfilling its most important purpose: keeping its citizens safe." The project, nearly two years in the making, includes detailed interactive graphics and maps.

Last week, President Obama nominated Army Maj. Gen. Robert Harding to head the Transportation Security Administration, but Harding's ties to several TSA contractors via Harding Security, a firm he founded in 2003, have raised ethics concerns.   "A review of Harding Security's business activities by CongressDaily showed that of 21 companies listed on the firm's Web site as its 'clients and partners,' several firms, including Lockheed Martin Corp., L-3 Communications, SAIC, CACI, QinetiQ and General Dynamics Corp., have done business with TSA."

Analysis of a Federal Aviation Administration (FAA) database made available to ABCNews.com showed that "a notorious drug kingpin, a convicted arms trafficker and several other individuals linked to aviation-connected crimes continue to hold FAA pilots licenses," according to a report by Eric Longabardi and Joseph Rhee. The findings raise questions in the efforts of the Transportation Security Agency (TSA) and the FAA in purging individuals who pose a threat to national security.

Jerry Mitchell of The Clarion-Ledger (Jackson, Miss.) reports that documents obtained by the paper show "the U.S. attorney's office in Oxford targeted convenience store operators in north Mississippi, many of Middle Eastern descent, despite a lack of any connection to terrorism." While no links to terrorism were found, the "Convenience Store Initiative" netted other criminal misconduct such as the sale of excessive amounts of pseudoephedrine — a drug used in meth production. The initiative was praised by the Justice Department in the Bush administration.

G.W. Schulz of California Watch found widespread waste and mismanagement of homeland security grants awarded to agencies throughout the state of California. Schulz reviewed thousands of pages of documents from state monitoring reports and found scores of problems and questionable purchases.

G.W. Schulz of the Center for Investigative Reporting investigated the policing tactics used during Republican National Convention in St. Paul, Minn. last year. "Officials took unprecedented advantage of new laws to halt potential subversives before they attack. But the effort resulted in heavy-handed tactics, according to interviews and documents obtained by the Center for Investigative Reporting."

"Civilian workers who suffered devastating injuries while supporting the U.S. war effort in Iraq and Afghanistan have come home to a grinding battle for basic medical care, artificial limbs, psychological counseling and other services," according to a joint investigation by ABC News, the Los Angeles Times and ProPublica. The report says serious claims are routinely denied by the the taxpayer-funded policies held by civilian contractors while companies like American International Group (AIG) have turned hundreds of millions of dollars in profit on these policies.

Adam Goldman and Randy Herschaft tell the story behind the hunt for Abu Ibrahim, a bombmaker who has eluded authorities for decades.  Long forgotten and even presumed dead by some, Ibrahim is very much alive, according to an Associated Press investigation.

The Center for Investigative Reporting files ongoing reports about what viewers don't see in the ABC reality TV series, "Homeland Security USA," which G.W. Shultz characterizes as " 'Cops'-style, heart-pounding segments of border agents drawing their weapons on a suspect or airport security seizing smuggled narcotics" with an occasional pause "to focus briefly on the warm personal story of a homeland security employee." The show's vignettes are contrasted with more numerous reports about the difficulties of immigrants seeking residency.

In an interview with The Washington Post's Bob Woodward, the official overseeing U.S. military commissions confirmed that treatment of a Guantanamo Bay detainee qualified as torture. "The public record of the Guantánamo interrogation of the detainee, Mohammed al-Qahtani, has long included what officials labeled abusive techniques, including exposure to extreme temperatures and isolation, but the Pentagon has resisted acknowledging that his treatment rose to the level of torture."