Today, President Obama announced his intention to nominate Jeh Johnson as the new head of the Department of Homeland Security. It's a surprise pick, after a long search that included everyone from TSA chief John Pistole to New York City's police chief, Ray Kelly. But while Johnson has been in and out of national politics for 15 years now, he’s kept a fairly low profile outside of military circles. He has a reputation as a canny military lawyer and a ruthless pragmatist. As he prepares to take the reins of one of the country’s most controversial agencies, that’s a good thing, but it also has a number of observers worried. What will Jeh Johnson mean for Homeland Security?

His big court battles have been about the politics of the military

The biggest change is that Johnson comes from the military, an unusual choice to head up a civilian agency. Like most of his predecessors, he's a lawyer by trade, but his national posts have been at the Air Force and the Department of Defense. Compare that to his three predecessors, Tom Ridge, Michael Chertoff, and Janet Napolitano. That's two governors and a prosecutor, perfect for running a civilian agency that was supposed to work hand-in-hand with the Department of Justice. Chertoff in particular had made his name leading the prosecution's case against Zacarias Moussaoui, a poster boy for the judicial side of the global war on terror.

A legal rationale for a messy, ad hoc solution

Johnson's rep is different. His big court battles have been about the politics of the military, whether it was defending drone strikes, pushing to repeal Don't Ask Don't Tell, or building a new Guantanamo court system. Those cases meant navigating the hermetic culture of the military and the wilds of international law. And in each case, Johnson was asked to build a legal rationale for a messy, ad hoc solution. If the Bush years were a taxi to the dark side, Johnson's project has been a slow stroll back towards the light.

But not all the way back. You don't get to be general counsel for the Pentagon by being an idealist, and for many civil libertarians, Johnson's arguments have done as much harm as good. Constructing the 2009 Guantanamo commissions is a perfect example. Johnson's reforms brought Guantanamo closer in line with the Geneva Conventions, providing more funding for defense counsel and more limitations on coerced testimony -- but Johnson's 2009 act did little to address the fundamental problems of the site. The commissions were still allowed to try children and "combatants" who hadn't been engaged in any hostilities. Working for a president who had campaigned on closing down the international prison, Johnson seemed like a spoiler, and his reforms seemed like an excuse for not doing more.

He believes there's nothing illegal about drone strikes on US citizens

Johnson's defense of drones walks a similar line. Many have been encouraged by his speeches, which attack government secrecy as counterproductive, and envision an eventual end to the government’s war against al Qaeda. But Johnson used those concessions to build a strong legal foundation for transnational drone attacks that could last long beyond our current conflict. Most crucially for someone about to take over a domestic agency, he believes there’s nothing illegal about drone strikes on US citizens. "Belligerents who also happen to be US citizens do not enjoy immunity," he said in a February 2012 speech. "The essential mission of the US military is to capture or kill an enemy. Armies have been doing this for thousands of years."

As head of Homeland Security, he’ll presumably be applying a similar ethos on American soil. On politics, it could turn out to be a smart choice: a pragmatic outsider to seize control of an agency that’s lost clout in Washington. But regaining the public’s trust after years of TSA debacles could be a harder sell, and Johnson’s Pentagon-bred instincts could make it a harder one. Even worse is the creeping sense that, at the NSA and elsewhere, the War on Terror has tricked the government into turning the military apparatus against its own public. If Johnson’s going to fight that impression, he’ll be facing an uphill battle.