It’s hard to know who to root for in the continuing scuffles between the Republican Congress, the White House and the CIA over the intelligence agency. The latest round–actually, it’s a postdated tussle–was triggered by a May 18, 2006 letter that Representative Peter Hoekstra, the Republican chairman of the House intelligence committee, sent to George W. Bush raising protests on three fronts: recent appointments at the CIA, the new Director of National Intelligence office, and the White House’s failure to brief Congress about certain covert programs, which Hoekstra didn’t name in his letter. (The letter was first disclosed by The New York Times on July 9.)

It was easy for some to see Hoekstra as a heroic reformer challenging secret government. named Hoekstra the “Truthdigger of the Week.” But the spy wars of Washington are not linear affairs and the battle lines murky. Is the CIA a rotting institution that failed prior to 9/11 and then provided Bush flawed intelligence to justify an invasion of Iraq? Or is it a bastion of risk-averse conventionalists who have undermined Bush’s ambitious, forward-looking national security agenda (which includes the Iraq war)? The CIA has been getting it from the left and the right in recent years. And it’s unclear whether the top tier of the agency ought to be backed or booted.

When Porter Goss, a Republican who preceded Hoekstra as chairman of the House intelligence committee, was CIA director, he placed his political aides in charge of the agency, and the career officers rebelled. Several of the most experienced CIA veterans–including Stephen Kappes, the director of operations, resigned rather than deal with the Goss crew. The CIA people viewed the Goss gang as hacks motivated by political concerns; Goss and his allies saw the CIA career leadership as bureaucrats resistant to change. (Goss resigned as CIA chief in May; he was replaced by General Michael Hayden, who, as the National Security Agency chief, was a longtime intelligence professional.)

Enter Hoekstra and his letter. What received the most attention was his charge that his committee had not been briefed about “some alleged Intelligence Community activities.” He added, “If these allegations are true, they may represent a breach of responsibility by the Administration, a violation of law, and, just as importantly, a direct affront to me and the Members o this committee.” Hoekstra did not say what secrets the White House had been keeping from him. Open-government fans cheered Hoekstra’s pointed reminder to Bush: the law says you cannot run covert programs on your own without telling Congress. And on Fox News Sunday, the day his letter was disclosed, Hoekstra said his letter had done the trick and that subsequently he was briefed about this intelligence activity–which he still would not identify. (Hoekstra is not much of a maverick; he has not rushed to hold public hearings on such matters as the controversial and arguably illegal NSA domestic wiretapping program.)

Another point Hoekstra made in his letter was important. He expressed his concern that the new DNI office has become a “large, bureaucratic, and hierarchical structure.” If there was a need for a DNI–which supposedly is supposed to coordinate the various intelligence agencies of the US government, including the CIA–there was no reason to create another intelligence bureaucracy. The intelligence community would benefit more from streamlining than from an expanding management. So score Hoekstra another point here.

But the first topic Hoekstra raised in his letter shows he can be loopy. Hoekstra voiced his displeasure over the selection of Hayden, an Air Force general, to be the CIA director, noting that he wanted a civilian to head a civilian agency. But what really ticked him off was the selection of Kappes to be the new number-two at the agency. Bringing back Kappes, Hoekstra wrote, would lead to “political problems” at the agency. What did Hoekstra mean by this? He explained: “I have been long concerned that a strong and well-positioned group within the Agency intentionally undermined the Administration and its policies. This argument is supported by the Ambassador Wilson/Valerie Plame events, as well as by the string of unauthorized disclosures from an organization that prides itself with being able to keep secrets.” Kappes, he added, is part of this group.

Hoekstra didn’t spell it out in his note. But what he was saying was that he believed a CIA cabal has tried to undercut Bush regarding the war in Iraq–that CIA officials opposed to the war plotted against the president and sought to undercut his case for war by leaking stories indicating that the intelligence cited by Bush and his aides on Iraq’s WMDs and purported connections to al Qaeda was not that strong. (Joe Wilson’s trip to Niger and subsequent op-ed piece declaring there had been nothing to the charge Iraq was seeking uranium there, the rightwing theory goes, was part of a deliberate CIA conspiracy against the White House.) Hoekstra also is probably thinking of the leaks about CIA secret prisons and the agency’s clandestine renditions of detainees to nations where abusive interrogation occurs.

So Hoekstra appears to be of the belief that the problem was not that Bush used flawed WMD intelligence to take the nation to war but that CIA leakers disclosed the flaws of the intelligence. This is a tad alarming, for every post-invasion review of the intelligence–including one conducted by Hoekstra’s own committee–found that the intelligence community was dead wrong on WMDs. A Senate intelligence committee review also concluded the CIA had been right to conclude there was no strong evidence that al Qaeda and Saddam Hussein were in cahoots. Hoekstra should realize that the important issue is not the leaks (which were true) but the misuse of the intelligence.

But Hoekstra still believes in Iraq’s WMDs. Last month, he joined with Republican Senator Rick Santorum to hype a 2003 Defense Department report that noted that about 500 weapons containing degrade mustard gas or sarin nerve agent had been found in Iraq. These weapons, though, were manufactured before the first Gulf War and were not evidence that Saddam Hussen had maintained a WMD program in the years before the invasion. A senior Pentagon official, quoted by Fox News, said that these weapons were not useable. “This does not reflect a capacity that was built up after 1991,” he said, noting the munitions “are not the WMDs this country and the rest of the world believed Iraq had, and not the WMDs for which this country went to war.” Yet Hoekstra and Santorum made it seem this discovery was significant. Hoekstra promised further investigation. “We are going to put additional pressure on the Department of Defense and the folks in Iraq to more fully pursue a complete investigation of what existed in Iraq before the war,” he said.

Let’s recap: Hoekstra was mad at Bush for keeping him out of the loop, and he warned the president about expanding the bloated intelligence capability. But he thinks the CIA is laced with politically-minded plotters who hold unfounded beliefs (such as there were no operational links between Saddam and Osama bin Laden) and who are working to thwart the national security policies of the nation. In Washington’s version of Spy Verus Spy, it can be difficult to know which–if any–side to cheer.