The naval shipyard at Hunters Point is the quietest neighborhood in San Francisco. Once a center for first commercial and then defense shipbuilding, the 866-acre site is now a graveyard for mess halls, railroad maintenance facilities, abandoned hangars. The shipyard has pristine bay views, and Hunters Point is blessed with a sunny microclimate, so it’s the perfect place for a stroll — as long as you’re not spooked by shattered buildings or eerie silence.

Or toxic chemicals. The shipyard is a Superfund site, considered one of the nation’s most contaminated sites. It’s the subject of an extensive, expensive environmental cleanup that has dragged on for decades. The finish date for the cleanup has shifted over the years — in 2011, The Chronicle reported that the U.S. Navy hoped to be done by 2017.

Now it says 2021 or 2022 seems more likely.

I went to the shipyard to find out why.

Like most stories about land in San Francisco, this one is complicated. Decades’ worth of petroleum fuels, heavy metals, PCBs and volatile organic compounds have leached into the hills’ serpentine rock and the bay’s sediment.

It wouldn’t be a short cleanup for any organization, but this one has still taken an extraordinarily long time. The Navy ceased active operations at the shipyard in 1974, started base cleanup in the late 1980s, and it’s still managed to transfer less than half of the parcels to Lennar Urban, the developer that’s building “a new story” at the site.

In 2010, the San Francisco Board of Supervisors approved a development plan of 10,500 new units, with retail and entertainment facilities. The first residents moved in last year.

“People do wonder why this has taken so long,” said Derek Robinson, environmental coordinator for the Navy. “This is a long process. We have to get multiple regulatory agencies — federal, state and local — to agree to what we’re doing. We have to be very transparent with the public. And we have to do it right.”

I don’t doubt that the process of getting approvals for a project like this is more akin to a tortoise than a hare — the amount of red tape Robinson mentioned made me wince — but I had to wonder.

Would San Francisco allow this kind of delay if the shipyard had been in, say, Pacific Heights?

Probably not. Let’s just be honest about the way political power works. Hunters Point is a historically African American, lower-income neighborhood that’s geographically separated from the rest of the city. It’s no accident that San Francisco’s Superfund site is there, no surprise that the cleanup hasn’t proceeded quickly.

And it’s no surprise either that the local community regards the cleanup crew with some suspicion.

“The community is one of the big challenges because there are fears, and I understand that,” Robinson said.

I asked Danielle Janda, the lead remedial project manager, about what people express as their greatest concern when the Navy hosts public tours. (These tours usually happen twice a year; see http://bit.ly/2bHNnqt for more information.)

“The landfill,” Janda said. “There are a lot of questions about why we don’t dig up the landfill and move it somewhere else.”

The landfill is one of the toughest spots to clean up. Located near a wetland area on Griffith Street at the bottom of a hill, it was the disposal spot for both garbage and industrial waste.

Cleaning up all of those chemicals has required the Navy to prevent water from getting into the landfill. But water drains downhill, and soaks into wetland areas. So they’ve built an underground wall around the landfill to prevent groundwater from seeping in. They’ve also covered it with a new layer of earth. Eventually the whole area will be revegetated with native grasses.

“It’s less disruptive than moving all of the earth around, potentially leaching chemicals into other areas,” Janda explained. “Plus, where would we put the waste?”

Understandable, from a scientific perspective. But maybe less understandable if you have to live there.

The problem at the shipyard is that the science of its cleanup doesn’t mesh neatly with its politics. Robinson explained that their work will never produce a “clean slate” where the earth is as clean as an Edenic garden.

It makes perfect scientific sense — there is no such thing as chemical-free earth. The Navy needs to scrub the shipyard’s environment until it’s safe for habitation. Safe doesn’t mean the past will disappear.

After spending the morning at the shipyard, I even understand why the cleanup is taking so long. It’s a huge site, production was dirty, and they have to deal with a Bay Area land process. The Navy is being painstaking, and I’d rather they get it done right than do it fast.

But politically, I can’t see any leader — at the city or federal level — allowing this agony to drag on for decades in any other San Francisco neighborhood. And that’s a problem science can’t fix.

Caille Millner is a San Francisco Chronicle staff writer. Email: cmillner@sfchronicle.com Twitter: @caillemillner