During the presidential campaign in 2008, Mr. Obama railed against the agency’s use of torture and secret prisons during the Bush administration, and shuttered the detention program during his first week in office. But he has empowered the agency in other ways — including allowing its director, not the White House, to make the final decisions about drone strikes in Pakistan.

“Many presidents tend to be smitten with the instruments of the intelligence community. I think Obama was more smitten than most,” said one former senior Obama administration official, speaking on the condition of anonymity to discuss classified intelligence matters. “This has been an intelligence presidency in a way we haven’t seen maybe since Eisenhower.” The C.I.A. had shifted from capturing and interrogating terrorism suspects to targeting them with armed drones even before Mr. Obama came to office. It was a tactic championed by Congress at the same time that lawmakers were beginning to criticize the agency’s detention and interrogation program.

The agency carried out its first drone strike in Pakistan in June 2004, weeks after a draft of a damning C.I.A inspector general report about abuses in the agency’s secret prisons began circulating in Washington. In the months that followed, the agency began to refashion itself not as a long-term jailer, but as a secret paramilitary force that could kill terrorism suspects with little controversy.

For the C.I.A., there were far fewer political costs associated with killing terrorists than with capturing and interrogating them. There have now been more than 400 drone strikes in Pakistan, according to statistics compiled by the Bureau of Investigative Journalism, and the operations have had broad support among Democrats and Republicans. And the C.I.A. continues to carry out drone strikes in Yemen, despite the Obama administration’s declared intention in May 2013 that the drone program be transferred to the Pentagon.

John O. Brennan, the C.I.A. director, said during his confirmation hearing in 2013 that he wanted to refocus the agency on traditional missions like espionage and analysis. But the effort has been slow going for a number of reasons. For instance, the congressional intelligence committees have vigorously tried to block transferring drone operations to the Pentagon — fighting to keep the C.I.A. in control of aspects of the program.

Mr. Johnson, the University of Georgia professor, was the Church Committee staff member who was eating lunch with Mr. Angleton in 1976 when he fulminated against an interfering Congress. In the years since then, he said during a recent interview, he has often met senior C.I.A. leaders who took a dim view of congressional oversight.

During one dinner he had with William J. Casey, the agency’s director during the Reagan administration who became enmeshed in the Iran-contra scandal, he said that Mr. Casey told him that the role of Congress was to “stay the [expletive] out of my business.” But as much as America’s spies might still complain about their overseers, the years since the Sept. 11 attacks have been an era of broad license — and hefty budgets — not just for the C.I.A., but also for the National Security Agency and other intelligence services. Neither the White House nor the American public has shown an inclination to change that.