In the last month, Texas prosecutors secured a dramatic conviction of former House Republican leader Tom DeLay, and the Justice Department announced it was not going anywhere in its long-standing inquiries into ethics violations involving Senator John Ensign, Representative Jerry Lewis, and a number of other prominent political figures (including DeLay). These developments have led to pointed criticism of the Justice Department’s public integrity section, whose nose has been badly bloodied by a number of disclosures of serious misconduct, including a criminal probe focused on its past leaders arising out of their botched handling of a case against Senator Ted Stevens.

The ever-astute Charlie Savage has recapped these developments with an assessment of the Justice Department’s woes:

The Justice Department has shut down a wave of high-profile investigations of members of Congress over the past few months, drawing criticism that the government’s premier anticorruption agency has lost its nerve after the disastrous collapse last year of its case against former Senator Ted Stevens…

“They’re gun-shy,” said J. Gerald Hebert, the executive director of the Campaign Legal Center, a nonpartisan group that seeks greater disclosure of how money influences politics. But in interviews, Jack Smith, chief of the Public Integrity Section at the Justice Department, and his supervisor, Lanny Breuer, the assistant attorney general for the Criminal Division, hotly contested the contention that prosecutors were in retreat from taking on Congressional corruption. “It’s just not the case that anyone is gun-shy,” Mr. Breuer said. “If a case cannot be brought, it’s because we’ve taken a hard look and made the determination that this case cannot be proved beyond a reasonable doubt. And with all due respect to those outside the department, they haven’t seen the evidence. They don’t know the materials, and we’ve looked at it all.”

The problems that the Department faces are deep-rooted, and the gear-shifting that is evidently underway is entirely appropriate. The issues go both to process and to policy. The Stevens case and a host of others revealed serious flaws in the public integrity process at Justice: as Judge Sullivan intimated, prosecutors had adopted a “victory at all costs” attitude that led to unethical corner-cutting and the suppression of exculpatory evidence. In cases around the country, and particularly in the South, local U.S. attorneys turned to public integrity prosecutions as a form of political score-settling—a problem that has been present in the American justice system for over two centuries, but that Main Justice has generally attempted to restrain. In the Bush era, however, this process appears to have been spurred rather than retarded by Main Justice.

The policy issues are equally tenacious. Justice pursued public corruption matters relying heavily on a theory of “theft of honest services,” stretching a statute beyond its logical breaking point, as the Supreme Court concluded in Skilling. Moreover, the great bulk of the truly dubious cases came out of the dark woods of election financing—in many cases with federal prosecutors attempting to criminalize practices that were permitted under state law. With the Supreme Court’s ruling in Citizens United, which opened the floodgates of money as political speech, the efforts to criminalize campaign funding abuses seem truly absurd. The Justice Department’s efforts have boomeranged. Rather than demonstrating that the Justice Department is a guardian of the highest standards of conduct, the Department and its prosecutors have grown ever more deeply mired in partisan political muck. The Department’s reputation now stands at a modern low, thanks to the political machinations demonstrated in the U.S. attorney’s scandal, prosecutions like those of Stevens, Siegelman, and Minor, and the validation of torture and abuse and warrantless surveillance in the service of unethical clients.

“Conduct that people think is reprehensible or immoral doesn’t mean it’s criminal,” Assistant Attorney General Lanny Breuer observes. Indeed, the solution to much of the public integrity conundrum lies in transparency of process—insuring that the public learns of the foibles and ethics lapses of political leaders and can make appropriate decisions guided by this information. This, however, is not the proper role of the Justice Department, which seems these days almost obsessed with safeguarding its own dark secrets and occasional brushes with criminality from public gaze.

The Department’s public integrity section is under new leadership—the most highly qualified it has seen in recent decades. It has seized the right moment for an internal reassessment of the approach to prosecuting public corruption. That should entail recognizing that dedication to fair process must take a center seat even if some scoundrels get off the hook as a result. This reassessment must include some introspection about mistakes and abuses of the past as well, because the most serious misjudgments in the public integrity arena relate to active cases in which the Justice Department is defending utterly indefensible positions. In the end, the Justice Department will also have to learn to operate in the harsh sunlight of public attention, disclosing its mistakes and striving to correct them. This is the essential path back to public trust after years spent straying in the wilderness.