Harvard University is set to face a federal court on Monday to argue that the Trump administration unlawfully withheld $2.6 billion from the renowned institution, marking a critical point in its conflict with the federal government.

If U.S. District Judge Allison Burroughs rules in favor of the university, the decision would overturn a series of funding freezes that eventually became full cuts as the Trump administration intensified its dispute with the nation’s oldest and wealthiest university. Such a ruling, should it be upheld, would restore Harvard’s extensive scientific and medical research operations and numerous projects that lost federal funds.

“This case involves the Government’s attempts to leverage the withholding of federal funding to control academic decision-making at Harvard,” the university stated in its complaint. “In essence, the choice presented to Harvard and other universities is straightforward: Let the Government oversee your academic institution or risk the institution’s capacity to pursue medical breakthroughs, scientific discoveries, and innovative solutions.”

A second lawsuit over the cuts filed by the American Association of University Professors and its Harvard faculty chapter has been consolidated with the university’s.

Harvard’s lawsuit accuses President Donald Trump’s administration of waging a retaliation campaign against the university after it rejected a series of demands in an April 11 letter from a federal antisemitism task force.

The letter demanded sweeping changes related to campus protests, academics and admissions. For example, the letter told Harvard to audit the viewpoints of students and faculty and admit more students or hire new professors if the campus was found to lack diverse points of view. The letter was meant to address government accusations that the university had become a hotbed of liberalism and tolerated anti-Jewish harassment on campus.

Harvard President Alan Garber pledged to fight antisemitism but said no government “should dictate what private universities can teach, whom they can admit and hire, and which areas of study and inquiry they can pursue.”

The same day Harvard rejected the demands, Trump officials moved to freeze $2.2 billion in research grants. Education Secretary Linda McMahon declared in May that Harvard would no longer be eligible for new grants, and weeks later the administration began canceling contracts with Harvard.

As Harvard fought the funding freeze in court, individual agencies began sending letters announcing that the frozen research grants were being terminated. They cited a clause that allows grants to be scrapped if they no longer align with government policies.

Harvard, which has the nation’s largest endowment at $53 billion, has moved to self-fund some of its research, but warned it can’t absorb the full cost of the federal cuts.

In court filings, the school said the government “fails to explain how the termination of funding for research to treat cancer, support veterans, and improve national security addresses antisemitism.”

The Trump administration denies the cuts were made in retaliation, saying the grants were under review even before the April demand letter was sent. It argues the government has wide discretion to cancel contracts for policy reasons.

“It is the policy of the United States under the Trump Administration not to fund institutions that fail to adequately address antisemitism in their programs,” it said in court documents.

The research funding is only one front in Harvard’s fight with the federal government. The Trump administration also has sought to prevent the school from hosting foreign students, and Trump has threatened to revoke Harvard’s tax-exempt status.

Finally, last month, the Trump administration formally issued a finding that the school tolerated antisemitism – a step that eventually could jeopardize all of Harvard’s federal funding, including federal student loans or grants. The penalty is typically referred to as a “death sentence.”