Earlier this week, the New York Times reported that “The CIA suspected that Mr. Snowden was trying to break into classified computer files to which he was not authorized to have access, and decided to send him home, according to two senior American officials.”

The CIA disputes this account:

“The C.I.A did not file any report on Snowden indicating that it suspected he was trying to break into classified computer files to which he did not have authorized access while he was employed at the C.I.A., nor was he returned home from an overseas assignment because of such concerns,” Todd Ebitz, an agency spokesman, said in the statement.

In dispute is what Mr. Snowden did on his computer, and the agency’s response to it. The two officials cited by The Times said the C.I.A. suspected Mr. Snowden was trying to gain access to classified computer files he was not authorized to view. But other officials on Friday characterized the activity as much less serious, not involving potential security violations.

It was unclear why there was a divergence of opinion.

These officials on Friday also said that Mr. Snowden left the C.I.A. of his own volition. But had he remained with the agency in Geneva, they said, Mr. Snowden faced a potentially time-consuming and critical internal inquiry prompted by his supervisor’s report, an investigation that was halted once he quit the C.I.A. in 2009 to join the N.S.A. as a contract employee at a military facility in Japan.

The first report said:

While it is unclear what exactly the supervisor’s negative report said, it coincides with a period of Mr. Snowden’s life in 2009 when he was a prolific online commenter on government and security issues, complained about civil surveillance and, according to a friend, was suffering “a crisis of conscience.”

So, it’s not too hard to connect the dots: it looks like the target of the CIA’s concern was not Snowden’s actions, but rather, his beliefs.