U.S. Supreme Court justices Samuel Alito, Jr., left, Sonia Sotomayor and Clarence Thomas listen to a question from law professor Kate Stith during a conversation at Yale University on Saturday. (Jessica Hill/AP)

It wasn’t the first time that Justice Clarence Thomas, the wayward son of Yale Law School, returned to his alma mater.

But this time, with two of his colleagues on the Supreme Court sitting beside him Saturday afternoon, he offered a message of reconciliation and humility very different from the bitter reminiscences of law school he has provided in past speeches and in his autobiography.

When Thomas was asked what advice he had given students privately earlier in the day, he answered: “I guess I told them not to do what I did.”

“I wish that I came here at a time when I could have been more positive because there was so much here that I walked right by, that I closed my eyes and my heart to.”

In a ceremony in cavernous Woolsey Hall, Yale bestowed the Award of Merit on the three Supreme Court justices who learned law in New Haven: Thomas, Class of 1974; Samuel A. Alito Jr. (’75); and Sonia Sotomayor (’79).

The three took part in a jolly ceremony that bordered on the self-congratulatory — Dean Robert Post marveled at the “tiny law school” that has had an “outsized influence on American life.”

But there’s no denying the impact of a place where portraits of Supreme Court justices line the walls. At one point in the ’70s, Thomas, Alito, Bill Clinton and Hillary Rodham walked the halls at the same time.

The justices — who law professor Kate Stith said had insisted on informality and called Sam, Sonia and Clarence — swapped admiring stories about each other and offered self-improvement tips.

Sotomayor said one of her attributes is her sense of “powerful concentration,” but acknowledged that the way that sometimes plays out during oral arguments — where she becomes a domineering figure — is bothersome to colleagues.

Alito, often a scowling presence on the bench who winces at comments he doesn’t like and could not resist an eye roll when Justice Ruth Bader Ginsburg dissented publicly from one of his majority opinions, displayed a sense of humor that Thomas said is often seen in private.

Asked to name a book he was reading, Alito deadpanned: “I have two books that are inspirational and I keep them on the table by my bed, and I try to read from them a little bit each night. It’s ‘My Grandfather’s Son’ and ‘My Beloved World.’ ” Those are the memoirs written by Thomas and Sotomayor, respectively.

But it was the words of Thomas that were most striking.

In his book, Thomas wrote that he turned down Harvard Law because it was too big and too conservative; Yale’s famous liberalism was more in line with the man who voted for George McGovern in 1972.

But Thomas, with a wife and a child, seemed not to fit in. “I was at Yale, but I wasn’t of Yale,” he said later. “I didn’t have that pedigree.”

He roamed campus in overalls and black boots, and on Saturday declared himself as being cynical and negative.

Thomas came to believe that the fact that affirmative action had played a role in his acceptance to Yale tainted his achievement in the minds of potential employers.

“I’d learned the hard way that a law degree from Yale meant one thing for white graduates and another for blacks, no matter how much anyone denied it,” Thomas wrote. (Other black students in his class disagree with Thomas’s assessment and said they had no trouble finding jobs with the prestigious law firms that descend upon elite schools.)

Thomas wrote: “As a symbol of my disillusionment, I peeled a fifteen-cent price sticker off a package of cigars and stuck it on the frame of my law degree to remind myself of the mistake I’d made by going to Yale.”

Thomas has not changed his mind about affirmative action, but the law school has made concerted efforts to bring back into the fold a graduate who sits on the Supreme Court. Thomas, too, said he has learned to “forgive and forget, to turn and move on.”

Thomas has been back to New Haven before, but Saturday’s ceremony was the most public reconciliation. The justice said the event was “far more special” than his graduation and that he is “more idealistic now than I was back then.”

Post said there were some commonalities among the three justices. None came from families of lawyers. Alito’s parents were the first in their families to go to college, while Sotomayor and Thomas came from poverty.

But they were different presences at Yale. Alito was the shy conservative everyone remembered as a practicing Catholic. Post said Alito was known for sitting in the front row, never raising his hand or taking notes, impressing everyone when called upon.

Focused and serious, he won awards each year at Yale for his scholarly work and legal ability. His former roommate told reporters at the time of Alito’s nomination that he doesn’t remember Alito dating. “There are no anecdotes,” he said.

A couple of years ago, Alito had a Federalist Society dinner crowd laughing as he recalled that he was assigned to the constitutional law class taught by the liberal Charles Reich rather than conservative icon Robert Bork. Yale would not allow him to switch.

“I was forced to teach myself,” he said.

Alito told the crowd that during the years he and Thomas were the only Yalies on the Supreme Court, he could only imagine the thoughts of Yale’s liberal professoriate: “Where did we go wrong?”

On Saturday, Alito said the remembrances of his performance at Yale might be exaggerated with time. “But it sounds good, so I’m not going to deny it,” he said.

Nor was there mention of what was Sotomayor’s most notable moment at Yale: a complaint she filed after she felt insulted by an on-campus recruiter from a prestigious Washington law firm.

After asking Sotomayor whether she believed in affirmative action, Sotomayor said the law firm partner asked her: “Don’t you think it’s a disservice to minorities, hiring them without the necessary credentials, knowing you’ll have to fire them a few years later?”

Sotomayor filed a formal complaint with the school, and a student-faculty panel negotiated a full apology from the firm.

“News of the incident flared across campus and divided the school into camps — those who thought I had made too much of some offhand comments, jeopardizing Yale’s relationship with an important employer of its graduates, and those who were solidly in support of my action,” she wrote in her memoir.

She and Thomas disagree on affirmative action. She saw the outreach from Ivy League schools as creating “the conditions whereby students from disadvantaged backgrounds could be brought to the starting line of a race many were unaware was even being run.”

But at Saturday’s event, Thomas and Sotomayor seemed to find some common ground, and their experiences as minorities at Yale seemed a bit more aligned.

Both said they were ill-prepared for what Yale offered. While clerking for a federal judge is common for graduates at elite law schools, neither said they were fully aware of it as an option.

“I must admit I did not get as much out of the law school as I should have, and that was simply because of my attitude,” Thomas said.

“Clarence,” Sotomayor responded, “I really didn’t know how to take full advantage of the law school.” Despite finishing Princeton with honors, she said, “I got to Yale, and I learned a deep sense of humility.”

“Yeah,” Thomas answered. “Oh, yeah.”