Now, a plan to prevent that from happening again is in limbo, after the city’s application for a $10 million grant to build a berm and flood wall was denied by the Federal Emergency Management Agency earlier this fall following six years of collaborative planning.

Ten months into a Trump administration where climate-related funds and programs have been targeted for cancellation or clawbacks, the rejection of a climate-related grant doesn’t come as a surprise.

It’s the framing of the rejection that caught city planners off guard.

The stated reason? FEMA cites Boston’s failure to respond to concerns raised by the federal agency — an accusation the city and locals engaged in the yearslong application process say just isn’t true. The concerns raised in the letter, including the technical feasibility of the project and its ability to mitigate flood risk, had already been addressed, they say.

“That is gaslighting,” Steve Hollinger, a Fort Point resident and longtime advocate for a sustainable neighborhood, said of the government response. “I think it’s obvious that they are casting blame intentionally.”

The plan — to build a 2,300-foot berm and flood wall with $10 million of city funds and $10 million from the federal government — was first hatched in 2019, in the wake of those devastating 2018 storms.

In response to FEMA’s rejection letter, Brian Swett, the city’s chief of environment, energy and open space, sent a letter outlining the various ways all of FEMA’s concerns had already been addressed.

“Given the risk of inaction to life, safety, property, and critical infrastructure, we are providing the attached summary of the recent and extensive coordination with FEMA and its consultant to provide you with confidence that issues raised in that analysis have been addressed,” he wrote.

Now, with a government shutdown, it’s not clear whether FEMA will reconsider its decision, which the agency said had been final.

Inquiries sent to the regional FEMA office and to its national headquarters were responded to with automatically generated messages indicating that inquiries would be responded to “once the government funding lapse is resolved.”

Even as the plans sit in limbo, the city and neighborhood advocates have continued to meet to discuss next steps. The memory of those 2018 storms remains fresh.

When the storms hit, they were a sign of what the city knew was coming. Two years earlier, a city report, called “Climate Ready Boston” had warned that coastal flooding was among the most significant climate risks facing the city. But in the intervening years — and in the years following those 2018 storms — development in the Fort Point and Seaport neighborhoods boomed.

A flood wall wouldn’t solve all of the area’s flooding problems, but it would buy the area time while developers along the coastline beefed up properties and completed plans to build climate-ready real estate.

What’s more, the protections from the structure would extend beyond the neighborhood. As sea levels continue to rise and storms get stronger with climate change, modeling shows that the Fort Point Channel is a flood entry pathway for larger areas of South Boston.

“This shoreline somehow has to find its way to be protected, because it [Fort Point] is lower than what’s across the channel,” said Tom Ready, a board member of the Fort Point Neighborhood Association. “The water is just going to spill into the neighborhood.”

The structure would extend along the southeast edge of the Fort Point Channel, roughly between Necco Street and Dorchester Avenue. The project would also include deployable flood walls that could be added during high-risk events and later removed.

For six years, the city corresponded monthly with FEMA, working on the project’s specs, ensuring the city was taking into account all possible flood paths — of which there are several — before committing to this solution.

“The objective was that our project would be in the ground and completed within probably two years,” said Richard McGuinness, deputy director for climate change and environmental planning at the city of Boston’s Planning Department.

Now, it’s not clear what will happen, but the city is considering its next steps.

Hopefully, city officials say, FEMA will reconsider its decision in light of their response. If not, they may have to make due with having just half the budget, and figure out a plan b.

“We are actively looking at alternatives to provide near-term flood protection for the Fort Point neighborhood, that would be paid for by the city and be built in the short term,” said Christopher Osgood, Boston’s director of the Office of Climate Resilience.

Tom Ready, in Fort Point, said it’s a huge disappointment to be so close to the finish, after so many years of work, and have the application rejected. But he also said it wasn’t a surprise.

“We just view it as, you know, just another in the long line of problems that the state of Massachusetts and the city of Boston is having with the Trump administration,” he said.

Sabrina Shankman can be reached at sabrina.shankman@globe.com.