An old joke from Cold War days goes like this:
While briefing his admiral, a brisk young captain refers to the Soviets as "the enemy." The admiral interrupts: "Captain, the Soviets are our adversary. The Air Force is the enemy."
So it seems to be between the Army and the CIA.

Late Tuesday night, The New York Times published a stunning story. Ahmed Wali Karzai, the drug-dealing brother of Afghanistan’s President Hamid Karzai, has collected money from the Central Intelligence Agency for most of the past eight years.

The agency pays Mr. Karzai for a variety of services, including helping to recruit an Afghan paramilitary force that operates at the CIA’s direction in and around the southern city of Kandahar, Mr. Karzai’s home. ...
Mr. Karzai is also paid for allowing the CIA and American Special Operations troops to rent a large compound outside the city. ... Mr. Karzai also helps the CIA communicate with and sometimes meet with Afghans loyal to the Taliban.

The news in the Times story is not the information—Wali Karzai’s CIA ties have been widely rumored inside Afghanistan for years. The real news is the sourcing of that information to senior military officers, culminating in this on-the-record doozy from the chief of military intelligence in Afghanistan, Maj.-Gen. Michael Flynn: "The only way to clean up Chicago is to get rid of Capone."
What we have here is the Army’s shock-and-awe attack on the CIA’s relationship not only to Wali Karzai, but to his brother the president as well. Here’s Maj.-Gen. Flynn again:

If we are going to conduct a population-centric strategy in Afghanistan, and we are perceived as backing thugs, then we are just undermining ourselves.

Flynn’s big "if" clause is clarifying. Behind the Army-CIA dispute over Wali Karzai is a bigger and more consequential battle over two radically different approaches to the Afghan war.

The CIA has long been identified with what has come to be called a "counterterrorist" strategy, which seeks to identify the people inside Afghanistan who are deemed harmful to U.S. interests—and then kill or otherwise neutralize them. Reliable real-time information is indispensable to the success of such a strategy, and everyone agrees that Wali Karzai has information to sell. With such a strategy, other considerations, including good government for Afghanistan, fall to second or third place behind the supreme imperative of eliminating anti-American elements.
The counterterrorism approach appeals to many conservatives because it unsentimentally puts vital American interests first. And it appeals to some liberals (reportedly including Vice President Joe Biden) because it costs less in money and lives than a big war to stabilize the whole country.
The only drawback: We’ve been following that course now for eight years, over which time Afghanistan has become more unstable and more dangerous.
The alternative is the strategy the Army used with considerable success in Iraq and that it now wishes to try in Afghanistan: "counterinsurgency" or, as Flynn terms it, a "population-centric" approach. With that strategy, the security of the civilian population is the supreme strategic goal; the elimination of terrorism is a byproduct; and effective governance is an indispensable preliminary.
The corruption of Wali Karzai—and, for that matter, of his brother the president—actively impedes such a strategy. The Times quotes a former Afghan official who states a widely held view: "This government has become a factory for the production of Talibs because of corruption and injustice."
Counterinsurgency is often costly and usually slow. On the other hand, it has a good record of success, not only in Iraq. It is frequently claimed that guerilla wars are unwinnable (except by guerillas). But the most authoritative study calculates that government forces win as often as they lose. Among the successes: the U.S.-led suppression of the Huk insurgency in the Philippines in the 1940s and 1950s, the British suppression of a communist insurgency in Malaya in the 1950s and 1960s, and operations in Venezuela, Oman, and Central America.
So there’s our choice: Either we make a big investment aimed at securing peace or we pay a local bad guy to kill even worse guys. It’s the Army approach or the CIA approach. President Obama reportedly has almost made up his mind. It’s generally expected that he’ll split the difference between the two paths. That outcome will be described as a compromise. In reality, it’s dithering leading to a muddle.