Presumably, now that the story has broken, public pressure will compel some sort of explanation from the Department of Justice or the Obama administration. In the meantime, the AP's own story on the incident strongly suggests a theory for what happened: that the DoJ was looking for the source on the AP's May 2012 story about a successful CIA operation to thwart a Yemen-based terror plot, a sort of underwear bomber part two.
Here's what the AP says in its story about the subpoena:
The government would not say why it sought the records. U.S. officials have previously said in public testimony that the U.S. attorney in Washington is conducting a criminal investigation into who may have leaked information contained in a May 7, 2012, AP story about a foiled terror plot. The story disclosed details of a CIA operation in Yemen that stopped an al-Qaida plot in the spring of 2012 to detonate a bomb on an airplane bound for the United States.In testimony in February, CIA Director John Brennan noted that the FBI had questioned him about whether he was AP’s source, which he denied. He called the release of the information to the media about the terror plot an “unauthorized and dangerous disclosure of classified information.”
And here's a snip from the original May 2012 AP story that the agency believes may have started it all. Note that the story seems to cite both the FBI and CIA, as well as revealing that the bomb may not have been detectable by then-current airport security scanners:
US officials say the plot involved an "upgrade" of the underwear bomb that failed to detonate aboard a jetliner over Detroit on Christmas Day in 2009.This new bomb was also built to be used in a passenger's underwear but contained a more refined detonation system.The FBI is examining the latest bomb to see whether it could have passed through airport security and brought down an airplane, officials said. They said the device did not contain metal, meaning it probably could have passed through an airport metal detector. But it was not clear whether new body scanners used in many airports would have detected it.The would-be suicide bomber, based in Yemen, had not yet picked a target or bought his plane tickets when the CIA stepped in and seized the bomb, officials said. It is not immediately clear what happened to the alleged bomber.
So why was this such a big deal that it would compel a federal investigation and lead Brennan to call it "unauthorized and dangerous"? ThinkProgress's Hayes Brown explains:
AP learned of the plot a week before publishing, but “agreed to White House and CIA requests not to publish it immediately” due to national security concerns. But, by reporting the CIA’s involvement in foiling the plot, they put AQAP on notice that the CIA had a window into their activities. The AP’s reporting also led to other stories involving an operative in place within AQAP,and details of the operations he was involved in. That operative, it was feared, would be exposed and targeted by AQAP as retribution for siding with the United States.
In other words, the AP's prevailing theory seems to be that this investigation is aimed at identifying the source of a leak that may have compromised a CIA investigation into the Yemen-based group, al-Qaeda in the Arabian Peninsula. That's presently just a theory, though.