WASHINGTON — Just over a year after the Sept. 11 attacks, the C.I.A. dispatched the veteran clandestine officer Gina Haspel to oversee a secret prison in Thailand. Shortly after, agency contractors in the frantic hunt for the conspirators waterboarded a Qaeda suspect three times and subjected him to brutal interrogation techniques.
Ms. Haspel’s time running the prison, code-named Cat’s Eye, began her deep involvement in the agency’s counterterrorism operations and showed her willingness to take part in the agency’s rendition, detention and interrogation program, which shaped her career. She was a rising star until that dark chapter in C.I.A. history began to emerge publicly.
But under President Trump, her fortunes changed, and on Tuesday, he announced that he intended to name her director of the C.I.A.
With his elevation of Ms. Haspel, now the agency’s deputy director, Mr. Trump displayed a willingness to ignore the widespread denunciations of waterboarding, sleep deprivation, confinements in boxes and other interrogation techniques that were used by the C.I.A. more than a decade ago.
Her nomination is certain to reignite the wrenching debate over their use and the resulting psychological damage for terrorism suspects. Though lawmakers, human rights activists and others eventually condemned the interrogation methods as torture, the program had defenders. Among them was Mr. Trump, who vowed during his campaign to bring back waterboarding and once said “torture works,” though he later backed off that declaration.
Ms. Haspel, 61, would become the first woman to run C.I.A. if she is confirmed by the Senate.
“She is an outstanding person who also I have gotten to know very well,” Mr. Trump said on Tuesday in brief comments to reporters on the South Lawn of the White House.
During her Senate confirmation, Ms. Haspel will be forced to answer unsettling questions about waterboarding and her interactions with detainees. She will probably have to answer whether she would agree to reinstate waterboarding as the president has suggested and whether she believes that torture is an effective way to extract information from terrorism suspects.
“I don’t envy her trying to get through confirmation,” said Robert Eatinger, the former top lawyer in the C.I.A.’s Counterterrorism Center. “It’s going to be the first chance for senators to have someone intimately involved in the program in front of them to answer questions. I think they’ll take full advantage of that opportunity.”
Senators who were deeply critical of the interrogation program could stand in Ms. Haspel’s way. Senator Dianne Feinstein, Democrat of California and the former chairwoman of the Senate Intelligence Committee, oversaw its investigation into the program. The resulting 2014 report found that the program was deeply flawed and those involved portrayed it as more effective than it was, misleading policymakers. The extent of Ms. Haspel’s role in the program is not known; only the report’s executive summary was released, and it obscured the identities of agency operatives.
Ms. Feinstein has remained silent on whether she would block Ms. Haspel’s nomination but told reporters on Tuesday that the two women had worked together since Ms. Haspel ascended to the C.I.A.’s No. 2 post in February 2017.
“Since my concerns were raised over the torture situation, I have met with her extensively, talked with her,” Ms. Feinstein said. “She has been, I believe, a good deputy director. She seems to have the confidence of the agency, which is good.”
Senator John McCain, Republican of Arizona, who was held prisoner during the Vietnam War and tortured for five and a half years, demanded that Ms. Haspel publicly explain her role in the interrogation program.
“The torture of detainees in U.S. custody during the last decade was one of the darkest chapters in American history,” he wrote on Twitter. “The Senate must do its job in scrutinizing the record & involvement of Gina Haspel in this disgraceful program.”
Ms. Haspel was also embroiled in another dark episode in the C.I.A.’s interrogation program.
In 2005, Jose Rodriguez, then the head of the agency’s clandestine service, ordered the destruction of videotapes of the waterboarding sessions. Ms. Haspel, serving as Mr. Rodriguez’s chief of staff, was a strong advocate for getting rid of the tapes, former C.I.A. officers said.
Years later, when the C.I.A. wanted to name Ms. Haspel to run clandestine operations, Ms. Feinstein blocked the promotion over Ms. Haspel’s role in the interrogation program and the destruction of the tapes.
Amy Jeffress, a national security aide to former Attorney General Eric H. Holder Jr. who served in London for the Justice Department while Ms. Haspel was C.I.A. station chief there, defended her.
“She will be criticized for her role in the interrogation program, but my experience from working with her is that she has learned from those mistakes and will be a thoughtful and conscientious leader of the C.I.A.,” Ms. Jeffress said.
Ms. Haspel was described former agency operatives and F.B.I. agents who worked with her as apolitical, a tough intelligence professional and direct but collegial. She has successfully managed sometimes difficult relationships with foreign intelligence services and the occasional grumpy F.B.I. agent.
She has succeeded in an agency traditionally dominated by men. After joining the C.I.A. in 1985, she was assigned to the Central European Division. She spent long stretches overseas, including in Turkey and Central Asia, before ascending to station chief in New York, where she was posted when Osama bin Laden was killed and worked closely with the F.B.I. as the agencies combed through files taken from his compound.
She has held two of the top three jobs in the clandestine service and twice ran the C.I.A.’s station in London, a post made all the more important by the agency’s relationship with MI6, the British intelligence service.
But her role in fighting terrorism is certain to draw the most scrutiny as her confirmation hearing looms.
After the Sept. 11 attacks, the C.I.A. launched a desperate hunt around the globe to find those responsible. In 2002, agency operatives working with Pakistani authorities captured a Qaeda suspect, Abu Zubaydah, and ferried him to the C.I.A. prison in Thailand. He was harshly interrogated and waterboarded at least 83 times in one month, sent to the brink of death, revived and questioned over and over.
Ms. Haspel arrived to run the prison in late October 2002, after the harsh interrogation of Mr. Zubaydah, a former senior C.I.A. official said. In mid-November, another Qaeda suspect, Abd al-Rahim al-Nashiri arrived. Mr. Nashiri, accused of bombing the U.S.S. Cole, was the man who was waterboarded three times.
After the prison closed in early December 2002, former officials said, Ms. Haspel returned to the Counterterrorism Center outside Washington as an operations officer.
Of the many difficult jobs she has held her career, former agency officials said, running the C.I.A. and managing the president would likely prove to be the hardest.
Ms. Feinstein said her support would hinge on the outcome of a meeting with Ms. Haspel, who contacted Ms. Feinstein on Tuesday morning to request one. Ms. Feinstein declined to detail what she would ask and what assurances she might seek in exchange for her support of Ms. Haspel’s confirmation.
“There is a difference,” Ms. Feinstein said, “between the second spot and the top spot.”