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A federal judge Thursday said she was “inclined to extend” an earlier ruling and order the Trump administration to restore an additional $500 million in UCLA medical research grants that were frozen in response to the university’s alleged campus antisemitism violations.

Although she did not issue a formal ruling late Thursday, U.S. District Judge Rita F. Lin indicated she is leaning toward reversing — for now — the vast majority of funding freezes that University of California leaders say have endangered the future of the 10-campus, multi-hospital system.

Lin, a judge in the Northern District of California, said she was prepared to add UCLA’s National Institutes of Health grant recipients to an ongoing class-action lawsuit that has already led to the reversal of tens of millions of dollars in grants from the National Science Foundation, Environmental Protection Agency, National Endowment for the Humanities and other federal agencies to UC campuses.

The judge’s reasoning: The UCLA grants were suspended by form letters that were unspecific to the research, a likely violation of the Administrative Procedure Act, which regulates executive branch rulemaking.

Though Lin said she had a “lot of homework to do” on the matter, she indicated that reversing the grant cuts was “likely where I will land” and she would issue an order “shortly.”

Lin said the Trump administration had undertaken a “fundamental sin” in its “un-reasoned mass terminations” of the grants using “letters that don’t go through the required factors that the agency is supposed to consider.”

The possible preliminary injunction would be in place as the case proceeds through the courts. But in saying she leaned toward broadening the case, Lin suggested she believed there would be irreparable harm if the suspensions were not immediately reversed.

The suit was filed in June by UC San Francisco and UC Berkeley professors fighting a separate, earlier round of Trump administration grant clawbacks. The University of California is not a party in the case.

A U.S. Department of Justice lawyer, Jason Altabet, said Thursday that instead of a federal district court lawsuit filed by professors, the proper venue would be the U.S. Court of Federal Claims filed by UC. Altabet based his arguments on a recent Supreme Court ruling that upheld the government’s suspension of $783 million in NIH grants — to universities and research centers throughout the country — in part because the issue, the high court said, was not properly within the jurisdiction of a lower federal court.

Altabet said the administration was “fully embracing the principles in the Supreme Court’s recent opinions.”

The hundreds of NIH grants on hold at UCLA look into Parkinson’s disease treatment, cancer recovery, cell regeneration in nerves and other areas that campus leaders argue are pivotal for improving the health of Americans.

The Trump administration has proposed a roughly $1.2-billion fine and demanded campus changes over admission of international students and protest rules. Federal officials have also called for UCLA to release detailed admission data, ban gender-affirming healthcare for minors and give the government deep access to UCLA internal campus data, among other demands, in exchange for restoring $584 million in funding to the university.

In addition to allegations that the university has not seriously dealt with complaints of antisemitism on campus, the government also said it slashed UCLA funding in response to its findings that the campus illegally considers race in admissions and “discriminates against and endangers women” by recognizing the identities of transgender people.

UCLA has said it has made changes to improve campus climate for Jewish communities and does not use race in admissions. Its chancellor, Julio Frenk, has said that defunding medical research “does nothing” to address discrimination allegations. The university displays websites and policies that recognize different gender identities and maintains services for LGBTQ+ communities.

UC leaders said they will not pay the $1.2-billion fine and are negotiating with the Trump administration over its other demands. They have told The Times that many settlement proposals cross the university’s red lines.

“Recent federal cuts to research funding threaten lifesaving biomedical research, hobble U.S. economic competitiveness and jeopardize the health of Americans who depend on cutting-edge medical science and innovation,” a UC spokesperson said in a statement Thursday. “While the University of California is not a party to this suit, the UC system is engaged in numerous legal and advocacy efforts to restore funding to vital research programs across the humanities, social sciences and STEM fields.”

A ruling Lin issued in the case last month resulted in $81 million in NSF grants restored to UCLA. If the UCLA NIH grants are reinstated, it would leave about $3 million from the July suspensions — all Department of Energy grants — still frozen at UCLA.

Lin also said she leaned toward adding Transportation and Defense department grants to the case, which run in the millions of dollars but are small compared with UC’s NIH grants.

The hearing was closely watched by researchers at the Westwood campus, who have cut back on lab hours, reduced operations and considered layoffs as the crisis at UCLA moves toward the two-month mark.

In interviews, they said they were hopeful grants would be reinstated but remain concerned over the instability of their work under the recent federal actions.

Lydia Daboussi, a UCLA assistant professor of neurobiology whose $1-million grant researching nerve injury is suspended, observed the hearing online.

Aftewards, Daboussi said she was “cautiously optimistic” about her grant being reinstated.

“I would really like this to be the relief that my lab needs to get our research back online,” said Daboussi, who is employed at the David Geffen School of Medicine. “If the preliminary injunction is granted, that is a wonderful step in the right direction.”

Grant funding, she said, “was how we bought the antibodies we needed for experiments, how we purchased our reagents and our consumable supplies.” The lab consists of nine other people, including two PhD students and one senior scientist.

So far, none of Daboussi’s lab members have departed. But, she said, if “this goes on for too much longer, at some point, people’s hours will have to be reduced.”

“I do find myself having to pay more attention to volatilities outside of our lab space,” she said. “I’ve now become acquainted with our legal system in ways that I didn’t know would be necessary for my job.”

Elle Rathbun, a sixth-year neuroscience PhD candidate at UCLA, lost a roughly $160,000 NIH grant that funded her study of stroke recovery treatment.

“If there is a chance that these suspensions are lifted, that is phenomenal news,” said Rathbun, who presented at UCLA’s “Science Fair for Suspended Research” this month.

“Lifting these suspensions would then allow us to continue these really critical projects that have already been determined to be important for American health and the future of American health,” she said.

Rathbun’s research is focused on a potential treatment that would be injected into the brain to help rebuild it after a stroke. Since the suspension of her grant, Rathbun, who works out of a lab at UCLA’s neurology department, has been seeking other funding sources.

“Applying to grants takes a lot of time,” she said. “So that really slowed down my progress in my project.”

Despite a stinging rebuke from a federal judge Thursday, military forces deployed in Los Angeles will remain under presidential control through the weekend, setting up a series of high-stakes showdowns.

On the streets of Los Angeles, protesters will continue to be met with platoons of armed soldiers. State and local officials remain in open conflict with the president. And in the courts, Trump administration lawyers are digging deep into case law in search of archaic statutes that can be cited to justify the ongoing federal crackdown — including constitutional maneuvers invented to enforce the Fugitive Slave Act of 1850.

Many legal scholars say the current battle over Los Angeles is a test case for powers the White House has long hoped to wield — not just squelching protest or big-footing blue state leaders, but stretching presidential authority to its legal limit.

“A lot rides on what happens this weekend,” said Christopher Mirasola, a professor at the University of Houston Law Center.

By staying the order that would have delivered control of most troops back to California leaders until after the weekend, the 9th Circuit Court of Appeals left the Trump administration in command of thousands of National Guard troops and hundreds of Marines ahead of the nationwide “No Kings” protests planned for Saturday.

The Trump administration claimed in court that it had the authority to deploy troops to L.A. due to protesters preventing ICE agents from arresting and deporting unauthorized immigrants — and because demonstrations downtown amounted to “rebellion against the authority of the Government of the United States.”

But U.S. District Court Judge Charles Breyer of San Francisco wrote Thursday that Trump had steamrolled state leaders when he federalized California’s troops and deployed them against protesters.

“His actions were illegal — both exceeding the scope of his statutory authority and violating the Tenth Amendment to the United States Constitution,” Breyer wrote.

While ICE “was not able to detain as many people as Defendants believe it could have,” it was still able to uphold U.S. immigration law without the military’s help, Breyer ruled. A few belligerents among thousands of peaceful protesters did not make an insurrection, he added.

“The idea that protesters can so quickly cross the line between protected conduct and ‘rebellion against the authority of the Government of the United States’ is untenable and dangerous,” the judge wrote.

The 9th Circuit stayed Breyer’s ruling hours after he issued a temporary restraining order that would have allowed California leaders to withdraw the National Guard soldiers from L.A.

The pause will remain in effect until at least Tuesday when a three-judge panel — made up of two appointed by President Trump and one by former President Biden — will hear arguments over whether the troops can remain under federal direction.

The court battle has drawn on precedents that stretch back to the foundation of the country, offering starkly contrasting visions of federal authority and states’ rights.

The last time the president federalized the National Guard over the objections of a state governor was in 1965 when President Lyndon B. Johnson sent troops to protect Martin Luther King Jr. and the Selma to Montgomery March in defiance of then-Gov. George Wallace.

But sending troops in to assist ICE has less in common with Johnson’s move than it does with President Millard Fillmore’s actions a century earlier, Mirasola said. Beginning in 1850, the Houston law professor said, Fillmore sent troops to accompany federal marshals seeking to apprehend escaped slaves who had fled north.

Trump’s arguments to deploy the National Guard and Marines in support of federal immigration enforcement efforts rely on the same principle, drawn from the “take care” clause of Article II of the Constitution, Mirasola said. He noted that anger over the military’s repeated clashes with civilians helped stoke the flames that led to the Civil War.

“Much of the population actively opposed enforcement of the Fugitive Slave Act,” the professor said.

Some analysts believe Trump strategically chose immigration as the issue through which to advance his version of the so-called “unitary executive theory,” a legal doctrine that says the legislature has no power and the judiciary has no right to interfere with how the president wields control of the executive branch.

“It’s not a coincidence that we’re seeing immigration be the flash point,” said Ming Hsu Chen, a professor at the UCSF Law School. “Someone who wants to exert strong federal power over immigration would see L.A. as a highly symbolic place, a ground zero to show their authority.”

Chen, who heads the Race, Immigration, Citizenship, and Equality Program at UCSF Law, said it’s clear Trump and his advisers have a “vision of how ICE can be emboldened.”

“He’s putting that on steroids,” Chen said. “He’s folding together many different kinds of excesses of executive power as though they were the same thing.”

Some experts point out that Judge Breyer’s order is limited only to California, which means that until it’s fully litigated — a process that can drag on for weeks or months — the president may attempt similar moves elsewhere.

“The president could try the same thing in another jurisdiction,” said Elizabeth Goitein, senior director of the Liberty and National Security Program at NYU’s Brennan Center for Justice.

“President Trump’s memorandum to deploy troops in Los Angeles made it very clear he thinks it’s appropriate … wherever protests are occurring,” Goitein said. “He certainly seems to think that even peaceful protests can be met with force.”

Experts said Breyer’s ruling set a high bar for what may be considered “rebellion” under the law, making it harder — if it is allowed to stand on appeal — for the administration to credibly claim one is afoot in L.A.

“It’s hard to imagine that whatever we see over the weekend is going to be an organized, armed attempt to overthrow the government,” Goitein said.

The Trump administration, meanwhile, hasn’t budged from its insistence that extreme measures are needed to restore order and protect federal agents as they go about their work.

“The rioters will not stop or slow ICE down from arresting criminal illegal aliens,” the Department of Homeland Security said in a news release this week, which included mugshots of several alleged criminals who had been arrested. “Murderers, pedophiles, and drug traffickers. These are the types of criminal illegal aliens that rioters are fighting to protect.”

Even after the 9th Circuit decision, the issue could still be headed to the Supreme Court. Some legal scholars fear Trump might defy the court if he keeps losing. Others say he may be content with the havoc wrought while doomed cases wend their way through the justice system.

“It’s a strange thing for me to say as a law professor that maybe the law doesn’t matter,” Chen said. “I don’t know that [Trump] particularly cares that he’s doing something illegal.”

Times staff writer Sandra McDonald contributed to this report.