First came a hotly-debated decision by Cooper Union to start charging its students after being tuition-free for generations.
Then came an investigation by the state attorney general into the school's management of its finances.
Over the past year, Cooper Union's reputation as a world-class training ground for engineers, architects and artists has taken a back seat to headlines about the investigation, a lawsuit over the imposition of tuition and the future of its president.
Some Cooper graduates and students hope all the turmoil results in more financial stability and maybe even a return to the tuition-free model that has been central to the school's unique, egalitarian character.
"We know that students have had to refuse our offer because they couldn't afford it," said Mike Essl, a Cooper Union alumnus and faculty member who is a plaintiff in the lawsuit over the decision to charge tuition starting with this year's freshman class. "That has never happened before in the history of Cooper Union."
The attorney general's investigation includes a look into the management of Cooper Union's prime asset, the land under the Chrysler Building.
Investigators are also questioning a $175 million loan, with the landmark skyscraper as collateral, used by Cooper trustees to finance a new engineering building.
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With an endowment of $735 million, Cooper Union is not in imminent danger of failing. But a leveling-off of rents from the Chrysler Building in the early 1990s triggered massive budget deficits, according to a report from Cooper Union President Jamshed Bharucha a few weeks ago.
According to the report, the accumulated deficits from fiscal year 1990 to fiscal year 2012 topped $300 million. Bharucha said the tuition-free model he inherited when he took over as president in 2011 was not sustainable "without a disruptive intervention."
State Attorney General Eric Schneiderman is seeking to mediate the lawsuit and will reportedly push for a review of whether the school can go back to being tuition-free.
"We're cooperating fully with the attorney general's office," said Cooper Union spokesman Justin Harmon, who refused to comment on a report that the trustees offered not to renew Bharucha's contract if it would help end the investigation.
Many alumni and students feel that luxuries like the new building and Bharucha's $650,000 salary are at odds with Cooper Union's history as a no-frills haven for strivers.
"Cooper never had the best facilities, the most high-end equipment, but they always had the smartest people," said Devora Najjar, a junior studying chemical engineering who is the student representative to the board of trustees. "You make do with what you have."
The school's rich history rivals the traditions of better-known colleges with sprawling campuses and football teams.
Cooper Union was founded in 1859 by industrialist Peter Cooper to give talented young people a good education that was "open and free to all." Discrimination based on ethnicity, religion, or sex was prohibited.
Abraham Lincoln gave his famous "right makes might" anti-slavery speech at Cooper Union in 1860; Thomas Edison took classes there, and the NAACP held its first public meeting there in 1909. More recently, President Barack Obama spoke there in 2010.
From the earliest days, classes were offered at no charge to students from working-class families. A 1902 gift from industrialist Andrew Carnegie allowed Cooper Union to sustain that model, keeping it tuition-free as other colleges' price tags outpaced inflation.
