As the United States Agency for International Development was being dismantled in early February, aid workers and officials in Washington and around the world set out to salvage what they could.

In the months since, there has been a widespread and under-the-radar effort to retain and restore some of the agency’s most critical work — including some projects favored by those who had the administration’s ear, a New York Times investigation shows.

Former President George W. Bush, who created the H.I.V./AIDS prevention program known as PEPFAR, called Secretary of State Marco Rubio. Leadership at the World Food Program called senators and ambassadors, and they said that millions of hungry people would die. Aid workers and foreign officials found programs that could be said to align with Mr. Trump’s America First agenda and flagged them for Republicans to pass on to the White House with a request to reinstate them.

The shell of U.S.A.I.D that is left today is the result of this chorus of pleas and negotiations, and of hasty decisions made by political leaders, many of whom had little experience in foreign aid.

The overhaul was a far cry from the comprehensive review to evaluate aid programs and realign them with U.S. foreign policy that Mr. Trump promised on his first day in office.

Aid workers said different departments frantically drafted their own lists of awards to keep or restore, but no one seemed to be looking at the big picture. Sometimes Mr. Rubio would sign off on a decision, only for staffers from Mr. Musk’s Department of Government Efficiency or other political appointees to determine the opposite. The piecemeal approach, aid workers said, ignored the reality that some programs relied on others to function.

U.S.A.I.D. employees and officials — including members of Congress who are supposed to provide oversight of the agency’s work — have said they are still struggling to decipher the administration’s goals for foreign aid.

This account is based on 70 interviews and dozens of internal documents and correspondence, and an analysis of both public and internal award databases.

The remaining awards are designed to address acute disease, hunger and other emergencies, and not areas like education, governance or jobs that are supposed to help countries avoid crises in the first place. Aid workers and experts said this is a short-sighted way to handle foreign aid that reflects a deep misunderstanding of the agency’s work and will have long-term consequences for Americans.

“You know what is not efficient? Putting out fires,” said Laura Meissner, a former U.S.A.I.D. contractor, whose work to manage humanitarian aid in multiple countries was terminated. “It’s way cheaper to stabilize people so they can weather the storm than to wait until they are destitute and their kids are malnourished.”

No rhyme or reason

In February, Elon Musk appeared in an X Spaces event in part to discuss DOGE’s work at U.S.A.I.D. “You have just got to get rid of the whole thing,” he said.

Vivek Ramaswamy, who helped create DOGE, was also on the call and offered a solution: “Let’s say something is cut that the people of this country just demand needs to exist again. It can always be voted back into existence.”

Mr. Musk agreed. “Well said, Vivek.”

Demands to return funding to certain U.S.A.I.D. programs were already underway.

The day after Mr. Musk’s talk, Senator Jerry Moran, Republican of Kansas, publicly urged Mr. Rubio to move American-grown food aid that was stuck in U.S. ports with no funding for shipment. In the weeks to follow, U.S. shippers and farmers met with members of Congress to explain the value of their lifesaving programs.

Many U.S.A.I.D.-supported organizations, including Catholic Relief Services and Mercy Corps, spoke with members of Congress. Several award recipients, including faith-based groups, had private meetings with Pete Marocco, who was managing the agency for Mr. Rubio. Other aid organizations sued the administration.

These efforts were far more frantic than standard lobbying on Capitol Hill. At the same time, U.S.A.I.D. staff members were pushing Trump-appointed officials inside the agency to restore dozens of terminated awards that provided lifesaving food or medicine or kept employees safe overseas.

Political leaders, who had told employees that they knew little about the agency’s programs, acknowledged in late February that some of these awards might have been cut in error, according to internal emails reviewed by The Times.

Then on March 2, a former U.S.A.I.D. official who oversaw global health programs leaked memos that estimated millions would suffer or die from disease if programs did not resume. Over the next day, more than 300 awards were restored, according to internal documents reviewed by The Times. More than 100 more would be “unterminated” in the days to follow.

The newly restored awards included U.S.-grown emergency food aid, disaster preparedness, programs to combat H.I.V./AIDS and malaria, and several awards in Jordan and Cuba.

A senior State Department official who was not authorized to speak publicly said that agency leaders had conducted a faster review than originally planned, after a federal judge ordered officials to reverse the president’s freeze on foreign aid programs.

The official added that recalibrations should be an expected part of any major overhaul and noted that a vast majority of the termination decisions remained in place. The agency declined to make officials available for an on-the-record interview.

U.S.A.I.D. staff members said they felt there was no rhyme or reason to any of it.

The idea was to destroy everything, said a global health security expert at U.S.A.I.D., who spoke on the condition of anonymity for fear of retaliation, as did most aid workers and other officials interviewed for this article. If someone complained, they would bring it back.

Smaller, local organizations were largely absent from the restorations. Without people in Washington to speak up for them, many were left behind.

“Many were wholly dependent on U.S.A.I.D.,” said Tom Hart, the president of InterAction, an alliance of global nongovernmental organizations. “Suddenly pulling the rug from beneath them hurts the idea of helping countries reach self-reliance, a goal the first Trump administration rightly sought.”

Not about fraud, inefficiency or cost

Despite its claims that “waste and abuse run deep” at U.S.A.I.D., the administration did not prioritize keeping programs that work to reduce fraud.

Instead, officials canceled contracts designed to prevent abuse, including awards for inspectors to watch over aid delivery in high-risk locations in more than a dozen countries.

Cost savings was not a significant factor in the administration’s decision making, either. In March, Mr. Rubio announced that officials had cut about 83 percent of the programs at U.S.A.I.D., but, in dollar terms, they cut programs that were worth less than half of the agency’s obligations.

Officials kept some of U.S.A.I.D.’s largest commitments and cut thousands of less expensive ones, an analysis of multiyear grants and contracts shows. The median kept award was worth $6 million, and 40 percent of these awards were worth $10 million or more.

Some were worth billions. For example, the Washington-based private development firm Chemonics retained two awards for global health supply chains focused on H.I.V. and malaria, worth over $6 billion and $2 billion, respectively.

The median cut award, by contrast, was worth just over $1 million. About a third of the cut awards were worth $100,000 or less.

In March, Mr. Marocco told officials privately that he planned to save $125 billion by cutting programs at both U.S.A.I.D. and the State Department. All together, the canceled awards at U.S.A.I.D. were worth an estimated $76 billion over several years, and $47 billion had already been committed to them.

It remains unclear what will happen to that money. An analysis of spending data shows the canceled awards had about $17 billion left unspent when DOGE took its ax to the agency.

If the overhaul wasn’t focused on fraud, efficiency or costs, there was one north star: a post on X from Mr. Rubio on March 10, which explained the government was keeping “approximately 1,000” U.S.A.I.D. programs. Agency staff members said they were told that they could recommend programs to restore — or even seek new funds for existing awards — but that they could never let the total count surpass 1,000.

Aid workers saw the post as Mr. Rubio retaking some control of the U.S.A.I.D. overhaul after DOGE had taken it too far.

Divisions between the secretary and Mr. Musk’s team became clear in April, when Jeremy Lewin, a DOGE staff member who became a top U.S.A.I.D. official, canceled dozens of the most critical emergency food awards that officials had already promised to keep. Mr. Rubio had just signed off on more funds for at least one of the awards, a rare step and a clear sign of its priority.

Within days of the cuts, Mr. Lewin asked agency employees to restore at least six of the awards, according to an email reviewed by The Times. He apologized for the back and forth, saying it was his fault.

“You have Secretary Rubio getting kind of made a fool of by DOGE because he has repeatedly said that they are going to protect these kinds of lifesaving programs. And then you have DOGE go out and basically countermand him,” said Jeremy Konyndyk, president of Refugees International and a former U.S.A.I.D. adviser to the Biden and Obama administrations. “It’s really unclear who is steering the bus.”

The senior State Department official said that all decisions had been made by U.S.A.I.D. and State Department officials in close consultation with Mr. Rubio, and that they made adjustments as priorities evolved.

Picking up after DOGE

Conservatives have long wanted to reform foreign aid and the layers of bureaucracy that stand between Washington and the people who benefit. But the enormous scope of the U.S.A.I.D. reduction, and the rushed and opaque way it was done, has privately concerned many Republicans.

Andrew Natsios, a former U.S.A.I.D. administrator under President George W. Bush, said that DOGE made a mess that has left gaps for China and Russia to fill.

“Our economy, our security and our way of life is dependent on our connection to the developing world and not just the rich world,” he said “And we have just lost our influence in the developing world.”

As Mr. Musk has stepped back from the spotlight, the remaining steps of the overhaul have been relatively calm and more strategic, according to internal correspondence reviewed by The Times and interviews with people familiar with the decision making. Officials are bringing the remaining U.S.A.I.D. awards under the umbrella of the State Department this summer, where plans for these programs could change again.

The bureaus that will absorb the awards are facing significant cuts too, and employees have expressed concern that they simply do not have the staff, resources or expertise to run them. They plan to terminate more awards and to let others expire.

After months of uncertainty, even the chosen projects are struggling to plan for the future.

One is a World Food Program contract in Kenya that helps feed 700,000 refugees from nearby conflicts. The program is nearly out of food, and while it remains on the list of active U.S.A.I.D. awards, it has not received any funding this year.

As a result, the program’s organizers have had to reduce the rations they provide.

“Do I feed more people for a shorter period of time, or do I feed fewer people who are more critical?” said Lauren Landis, the program’s country director in Kenya. “We haven’t made that decision yet.”