The relationship between The New York Times and its most famous source, Daniel Ellsberg, reads like a thriller, replete with clandestine meetings, top secret documents and a war raging in the background.

The connection was mutually beneficial. For Mr. Ellsberg, a former military analyst who died on Friday at age 92, exposing a secret government history about the Vietnam War changed how the nation thought about a conflict that he opposed. And the 1971 publication of the documents, which became known as the Pentagon Papers, burnished The Times’s reputation as a government watchdog.

Yet Mr. Ellsberg had conflicted feelings about The Times.

Mr. Ellsberg was happy with the prominent coverage The Times gave the Pentagon Papers — “their courage in doing that and the risks they undertook” — Mr. Ellsberg’s son Robert said in an interview. And he respected Neil Sheehan, the main reporter on the story, believing he picked the right person for the leak.

But the younger Mr. Ellsberg said his father “had some regrets and resentment about the way he felt he’d been treated, which he felt was very unnecessary.”

In particular, Mr. Ellsberg was unhappy about being misled by Mr. Sheehan. Mr. Ellsberg was also upset by the way The Times later conveyed in an article about how he had provided the documents.

Mr. Ellsberg and Mr. Sheehan discussed the Pentagon Papers at length in March 1971, during an hourslong conversation that stretched into the night. Mr. Ellsberg had smuggled the Pentagon Papers — all 7,000 pages of them — out of an office, past security guards, in the fall of 1969. He deputized Robert Ellsberg, who was then 13 years old, to help make copies.

Eventually, Mr. Ellsberg gave Mr. Sheehan access to the papers, but with a condition: Mr. Sheehan could study and take notes on the documents, but he couldn’t make copies of them.

Mr. Sheehan violated that agreement, making copies of the documents with the help of his wife, Susan Sheehan, a former writer for The New Yorker. Mr. Sheehan did not tell Mr. Ellsberg. Over the next several months, he misled Mr. Ellsberg about the newspaper’s timetable for publishing a story about the documents.

When The Times was closer to publishing its stories, Mr. Sheehan asked Mr. Ellsberg for a full copy of the documents, believing that the request would be interpreted as a sign that the newspaper was preparing to publish a story. But Mr. Ellsberg missed the signal. He provided the documents but was surprised when The Times published the first article disclosing the documents on June 13, 1971.

The Nixon White House demanded that the paper stop publishing the information contained in the documents. The Times prevailed in court against the Nixon administration, setting a precedent blunting prior restraint by the government. Later, the government sought jail time for Mr. Ellsberg. A judge threw out the case against Mr. Ellsberg, citing government misconduct.

Decades later, on the day Mr. Sheehan died, The Times published an article about how the Pentagon Papers leak had happened. The article was based mostly on an interview with Mr. Sheehan that took place in 2015, in preparation for his obituary, the first time he had spoken at length publicly about his role in obtaining the papers. He granted the interview on the condition that his account wouldn’t be revealed until after his death, according to Janny Scott, the reporter who wrote the article.

“That prevented me from being able to run his account by anyone, including Mr. Ellsberg, until after Mr. Sheehan’s death,” said Ms. Scott, who left the paper years before the article was published.

In the interview, Mr. Sheehan said he had misled Mr. Ellsberg about the timing of the article because he was concerned that Mr. Ellsberg was acting irrational and might do something to jeopardize the story. He said the documents were too important to leave in his hands.

Mr. Ellsberg disagreed with Mr. Sheehan’s characterization that he was afraid of jail time, and he was unhappy that he wasn’t given a chance to respond to that point and others in the article.

Mr. Ellsberg tweeted a complaint about the article shortly after it was published, noting that he had given Mr. Sheehan a copy of the documents before The Times published the first installment of the Pentagon Papers. Mr. Ellsberg later criticized his treatment by The Times in an interview with The New Yorker.

Mr. Ellsberg’s son said his father was always willing to give the documents to The Times if he had a commitment that the paper would publish them — even at the expense of going to prison.

“The effect of not telling him, among other things, was that he was caught unprepared with a copy of the papers in his apartment where the F.B.I. could have swept in and found them,” Robert Ellsberg said.

The New York Times said on Monday that it had no comment about Mr. Ellsberg’s complaints about the relationship.

Months after the article about Mr. Sheehan, Mr. Ellsberg was a part of The Times’s 50th anniversary package about the Pentagon Papers. He gave numerous comments for an oral history. He also did an interview with the opinion section and for a podcast.

Still, he remained puzzled by some of his interactions with the newspaper. He sat for numerous interviews in his final year, including with Jill Abramson, a former executive editor at The Times, and James Risen, a former reporter at The Times who now works for The Intercept. In both interviews, Ms. Abramson and Mr. Risen said, he expressed his frustration with The Times.

Neither interview has been published. Ms. Abramson had been in discussions with The Times to write a guest opinion column about Mr. Ellsberg’s relationship with the company, though The Times later ran an opinion piece from a staff writer instead. Mr. Risen said his article, also about Mr. Ellsberg’s relationship with The Times, would be published soon.

In his 2003 memoir, “Secrets,” Mr. Ellsberg made clear that he was excited by the culmination of the story he had helped set into motion. Once he heard that the first article was being published, he bought a copy of the Sunday paper late on Saturday night with his wife.

“We came up the stairs into Harvard Square reading the front page, with the three-column story about the secret archive, feeling very good,” Mr. Ellsberg wrote.

Benjamin Mullin

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