U.S. Transportation Secretary Elaine Chao, saying “character matters,” urged U.S. Merchant Marine Academy midshipmen to be “principled leaders” at a graduation ceremony Saturday that capped a year of turmoil and change at the 74-year-old Kings Point school.

Chao, leader of the agency that oversees the federal service academy, was the featured speaker at a commencement unlike any other over the decades.

Among the scores of seniors who walked across the stage on Tomb Field were seven who did not receive their diplomas — the result of a flurry of action in federal court last week in Central Islip. The seven, members of the men’s soccer team, sued for their ability to graduate after the academy’s superintendent, Rear Adm. James A. Helis, suspended the NCAA Division III soccer program amid an investigation into sexual misconduct by the Transportation Department’s Office of Inspector General.

For those seven, the black cylinders marked with the academy’s insignia did not contain bachelor of science degrees and merchant mariner credentials. Their cylinders were empty.

Under an order by U.S. District Court Judge Leonard Wexler, the students — whom Helis placed on “deferred graduate” status on June 2 — were allowed to participate in the ceremony, but their graduation materials were withheld pending the results of the inspector general’s investigation. The students, their lawyers and government attorneys have another court date on July 6.

U.S. Transportation Secretary Elaine Chao speaks during the 81st commencement exercises at the U.S. Merchant Marine Academy in Kings Point on Saturday, June 17, 2017. Photo Credit: Steve Pfost

Lawyers for the seven, reached after the ceremony, said their clients appreciated the opportunity to participate.

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“We certainly believe at the end of the day, they’ll have their certificates and all they’re entitled to receive,” said Michael Cassell, a Jericho attorney representing five of the students.

Chao, who said at her Senate confirmation hearing that supporting USMMA is a top priority, urged graduates to aspire to become strong leaders as they depart Kings Point, whether in the armed services or careers at sea.

“One of the clearest beacons you will find in carrying out your duties is the motto of the U.S. Merchant Marine Academy, which is ‘Acta non verba,’ or ‘Deeds, not words,’ ” Chao said. “Deeds will define your character, and character will determine your career and your legacy.”

The school has been roiled by threats to its accreditation, a campus culture pervaded by coercion, bullying and sexism, and years-long problems with sexual assault and sexual harassment, which led then-Transportation Secretary Anthony Foxx last year to order the first-ever suspension of Sea Year — the intensive training program that is a hallmark of the curriculum and required for graduation.

Midshipman Garrett Hargis rings the opening bell during the 81st commencement exercises at the U.S. Merchant Marine Academy in Kings Point on Saturday, June 17, 2017. Photo Credit: Steve Pfost

That suspension, denounced by many parents, alumni and the shipping industry, was lifted in March on all but some commercial vessels, after the implementation of reforms in the credentialing process for carriers.

Last year, the Middle States Commission on Higher Education, the school’s independent accreditor, placed the academy on warning for failing to comply with five of 14 academic benchmarks. The Philadelphia-based commission is expected this week to consider the school’s progress in meeting the quality standards and decide whether to revise its standing. USMMA remains accredited while on warning.

Chao, in her speech, said she is “a strong supporter of the U.S. Merchant Marine and the U.S. maritime industry,” drawing thunderous applause from the audience. The Syosset High School graduate worked some of her first government jobs in the Transportation Department during President Ronald Reagan’s administration.

She noted that her father, who was born in a small village near Shanghai, had long dreamed of visiting Kings Point. In a poignant moment, James S.C. Chao, 90, whom Helis described as among the youngest merchant mariners of his generation, stood and was recognized.

Helis, who shook hands with all of the graduates, said in his speech, “You must have the conviction and the courage to always choose the harder right over the easier wrong, to put the mission and the needs of those you were charged to lead ahead of your self-interests.”

Court documents and federal officials say the inspector general’s probe stemmed from an incident involving a freshman soccer player on a team bus on Sept. 10, the day that USMMA played the U.S. Coast Guard Academy in Connecticut.

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Six of the seven plaintiffs, in court papers, say upperclassmen “teased” the freshman members on the bus — “consistent with school tradition” — and say they did not participate in any misconduct toward the freshman. Their lawsuit says that the freshman believed he was doused with urine, while the plaintiffs said it “apparently” was water.

The plaintiffs joined in one case are Connor Culiver of Scottsdale, Arizona; David Burkhardt of Cutchogue; Michael Heckmuller of Cypress, California; Gavin Yingling of Salisbury, Maryland; Cory Maier of Hampton, Virginia; and Brennan Becker of Weston, Florida. The complaint of Timothy Hughes of upstate Ballston Lake, filed Friday, is separate.

Ronald Meister of Manhattan, the attorney for Becker, whose court filing says he was not on the bus, said Saturday, “We are pleased that the court ruled it was proper for the students who successfully completed their course of study to participate in the graduation exercises.”

Buffalo lawyer Anthony J. Kuhn, who is representing Hughes, said his client “was very excited” to graduate. “He put a lot into this. He worked very hard to get where he is,” Kuhn said. “Four years of schooling, and there’s a lot of requirements to be able to graduate from the Merchant Marine Academy. He’s completed every requirement.”