Center for Strategic Communication

Two names have emerged in the search for the next director of the Pentagon’s premier research agency. Problem is, one of them has ties to Solyndra, the controversial solar energy firm that embroiled the White House in a scandal. And this isn’t exactly the time for another controversy at the top of the Defense Advanced Research Projects Agency.

According to four knowledgeable sources, Arati Prabhakar and Reginald Brothers are among the leading candidates to succeed Regina Dugan as the leader of Darpa. Both are agency veterans with serious geek cred. Either would be a landmark appointment: Prabhakar would be the first Indian-American Darpa director, and Brothers would be the first African-American to hold the job.

Brothers, who has a Ph.D. in optical communications and spectroscopy from MIT, is a senior official in the Defense Department’s Acquisitions, Technology & Logistics directorate, in charge of science and technology programs. He’s also a Darpa alum: a former program manager in the Strategic Technology Office and then the director of advanced programs and technology, he spent time at defense giant BAE Systems before returning to the Pentagon.

Prabhakar, who earned a Ph.D. in applied physics from Caltech, founded the agency’s Microelectronics Technology Office before decamping to Silicon Valley in the ’90s. An adviser to the Department of Energy, Prabhakar recently left a job at the venture capital firm U.S. Venture Partners. The company bet big on Solyndra, a failed clean-energy concern that reaped hundreds of millions from government loans after its investors opened their wallets to President Obama.

While she worked on clean-technology investments before leaving the firm last fall, according to the Wall Street Journal, it’s “unclear whether Prabhakar was directly involved with the firm’s Solyndra stake.” Still, this is a presidential election year, and appointing Prabhakar would breathe new life into the Solyndra scandal, merited or not.

Reginald Brothers is in the running to lead Darpa. Photo: Department of Defense

The short version of that scandal: Solyndra, a now-defunct solar-energy company based in California, received over half a billion dollars in loan guarantees from the Department of Energy beginning in 2009. But when doubts emerged about the company’s financial viability, the Energy Department unusually restructured the terms of the loan so that private investors in the Solyndra, not the taxpayers, would be repaid first if the company went bottom-up. Last year, Solyndra filed for bankruptcy protection — after Obama declared “the future is here” during a visit to Solyndra’s factory floor.

That wasn’t all. ABC News and the Center for Public Integrity reported that one of the firm’s major investors, George Kaiser, raised over $50,000 for Obama’s 2008 presidential campaign. (Kaiser isn’t tied to U.S. Venture Partners.) Mitt Romney, Obama’s Republican challenger, called the Solyndra affair an example of “crony capitalism.”

Even if this wasn’t a presidential election year, it’s not exactly an opportune time for Darpa to have a director who was touched by a scandal. The last one, Regina Dugan, owned a firm, RedXDefense, that won $400,000 in contracts from Darpa while Dugan was director. Dugan recused herself from anything having to do with RedXDefense, but in the financial disclosure forms she filed upon assuming the directorship in 2009, she noted that she continued to own stock in RedX, and the firm owed her a quarter of a million dollars. That spurred a wide-ranging inquiry from the Pentagon’s inspector general into how Darpa awards its contracts. The investigation had yet to conclude when Dugan defected to Google earlier this year.

Again, it is unclear what ties Prabhakar actually has to Solyndra, or whether they ought to be a stumbling block for her prospective tenureship at Darpa. Both Prabhakar and Brothers are clearly qualified to run the blue-sky research agency. (Top Pentagon spokesman George Little declined to comment for this story.) But Darpa’s main function is to assess the far-out defense needs of the United States; explore how to meet those needs with emerging or even undeveloped technology; and pick promising companies to develop it. And that sounds uncomfortably like the Solyndra debacle.