On a balmy afternoon in late summer, Jim Price reaches into the body cavity of a striped bass and pulls out a spleen. The sixty-eight-year-old jewelry-store owner palpates the organ with long gloved fingers, checking for disease. Finding none, he sets it aside before turning his attention back to the carcass. “There’s something here,” he barks, as he slices into the stomach with a scalpel and his volunteer assistant Jerry moves in for a closer look.

Jerry is two decades younger, with bristly whiskers, a butcher’s smock, and a John Deere cap. In his cheek is a wad of chewing tobacco. The two are standing on a dock on an inlet of the Chesapeake Bay in Maryland, hunched over a metal table with a plastic tarp suspended over their heads to protect them from the sun. The heat doesn’t seem to faze them, nor does the stench emanating from the pile of filleted bass carcasses that fishermen have been dropping at their feet all day.

Price slides his finger along the stomach lining, a look of anticipation creasing his face. After careful prodding, he pulls out a silvery six-inch fish. “There,” he exhales. It is an Atlantic menhaden, a bony, oily fish that has been the subject of warring factions of fishermen and coastal communities for the better part of two centuries.

Price is a lifelong striped bass fisherman with no formal training as a scientist. Yet he has spent the last four decades cutting open bass stomachs in a kind of renegade ecological study, charting the precipitous decline of the lowly menhaden. Price’s interest in the species is indirect; menhaden aren’t prized by anglers. But they are prized by striped bass. The little fish has historically been the striper’s most significant source of protein and calories. In fact, menhaden are a staple in the diets of dozens of marine predators in the Atlantic and its estuaries, from osprey to bluefish to dolphin to blue crab. In a host of undersea food chains, menhaden—also known as pogy and bunker—are a common denominator. They have been called the most important fish in the sea.

Price began his study years ago when it became increasingly evident to him that the striped bass in the Chesapeake were quite literally starving. And so, at least once a week he dissects bass to see whether the fish ate recently before they died. He squeezes spleens to determine if the fish had mycobacteriosis, a serious infection related to malnutrition that affects more than 60 percent of the striped bass in the Chesapeake Bay. He relays his findings in a numerical code of his own devising. “Body fat is a ten, ovaries a two, spleen is okay, empty stomach,” he says gruffly, while his wife, Henrietta, dutifully transcribes his thoughts into a ledger. Four times out of fifty, he pulls a whole menhaden from a bass belly, weighing each one with a small scale.

Local sport fishermen are happy to help Price by leaving him the bones and innards of their catch, because his work confirms what anglers up and down the Atlantic coast know from direct experience: the menhaden are disappearing.

Like any good mystery, this one has a prime suspect. Across the Chesapeake and about sixty miles to the south of where Price stands, a seaside factory hums and buzzes, filling the small town of Reedville, Virginia, with the putrid smell of menhaden chum. The looming smokestacks, warehouses, and pretty much everything else on Reedville’s Menhaden Road are owned by Omega Protein, a publicly traded company headquartered in Houston with a long and storied history of industrial fishing in Atlantic waters.

The operation is high-tech. Spotter planes take off from Reedville’s tiny airstrip to circle swathes of ocean, looking for the telltale shadow of menhaden moving by the million just below the surface. Pilots radio Omega Protein’s fleet of nine refurbished World War II transport ships, one of which dispatches two smaller boats that surround the school with a giant net called a purse seine, drawing the fish tightly together using the mechanics of a drawstring sack, until all the members of the school can be sucked out of the ocean with a vacuum pump. The boats can “set” the net twelve to fifteen times a day; a vessel will return to port with millions of menhaden aboard.

Harvested by the billions and then processed into various industrial products, menhaden are extruded into feed pellets that make up the staple food product for a booming global aquaculture market, diluted into oil for omega-3 health supplements, and sold in various meals and liquids to companies that make pet food, livestock feed, fertilizer, and cosmetics. We have all consumed menhaden one way or another. Pound for pound, more menhaden are pulled from the sea than any other fish species in the continental United States, and 80 percent of the menhaden netted from the Atlantic are the property of a single company.

To determine whether or not Omega Protein is overfishing menhaden, the government relies on a set of methods and calculations that are mystifying in their complexity. Every time Omega’s captains return to the Reedville port, they report their daily “unload”—how many tons of fish they have removed from the water. Onshore, a government agent periodically examines a handful of fish scooped from the ship’s hold and uses them to estimate the size and age composition of the day’s catch. Information from these samples, collected over the course of the fishing season, are collated with the captain’s logs, and the data goes to a single scientist for processing at the National Oceanic and Atmospheric Administration’s (NOAA) fishery lab in Beaufort, North Carolina. There it is gathered together with harvest information from the handful of smaller companies that fish for menhaden along the coast to sell as bait, as well as trend data from a few independent scientific surveys. This stew of data is fed into a mathematical fishery assessment model that takes many scientists and several months to run. The process generates an estimate of how many eggs the current menhaden population is producing, compared to how many eggs there would be in an unfished, pristine environment. This information is handed over to a sleepy, part-time board of regulators called the Atlantic States Marine Fisheries Commission (ASMFC), who decide whether fish stocks are at a safe level or if there should be concerns about overfishing.

To the consternation of anglers like Price, the official science on menhaden has said the same thing for years: not to worry. This implacable wall of reassurance from the government has flown in the face of what countless people say they experience out on the water every day—from anglers reeling in malnourished game fish, to biologists who have witnessed population declines among birds that feed on menhaden, to the whale-watching charter captains who now struggle to find the menhaden schools around which humpbacks congregate. These groups can’t help but conclude that the population of menhaden is, in fact, declining fast. (I have spent the past year researching the Atlantic States Marine Fisheries Commission and advocating for the use of independent science in its regulatory decisions.) Many have accused the ASMFC of willful inaction and suspect the undue influence of regulators from Virginia, whose political bosses openly support Omega Protein, a major employer on the state’s Northern Neck. Since 2001, Omega Protein has contributed more than $220,000 in campaign contributions to Virginia politicians, including almost $60,000 to the current governor, Bob McDonnell, sometimes mentioned as a potential running mate for Mitt Romney. Yet such complaints have always been met by the same, debate stopping response from the ASMFC: “the science” says that the menhaden population is perfectly fine.

Over the last few years, however, the tables have been turned. In 2009, a routine methodological upgrade at NOAA—and the subsequent discovery of a few lines of faulty computer code—forced the start of a profound shift in the ASMFC’s estimates of menhaden stocks. Now, Price and his angler and environmental allies have the upper hand—at least for the moment. In response, Virginia politicians are threatening a bizarre countermove: seceding from the ASMFC, and thereby throwing the entire regulatory regime into disarray. The struggle for control of menhaden has suddenly been pulled out into the open water. How it plays out could determine the long-term ecological health of the Atlantic Ocean.

Menhaden were once so plentiful in the Atlantic that early pioneers described them as swimming in schools twenty-five miles long or more, packing themselves into bays and estuaries where they came to feed on dense schools of phytoplankton (algae and vegetable matter). Rutgers professor H. Bruce Franklin uncovered a trove of early accounts of menhaden for his book, The Most Important Fish in the Sea, like one from John Smith, who in 1608 encountered menhaden in the Chesapeake “lying so thick with their heads above the water, as for want of nets we attempted to catch them with a frying pan.”

In the 1860s, frying pans gave way to the purse seine, a device that enabled a boat to bag an entire school at a time. By 1876, half a billion pounds of menhaden were being processed in ninety-nine “reduction” factories along the Eastern Seaboard—so named for their way of breaking the fish down into raw materials. Menhaden were fueling an industrial boom: the oil in their flesh had replaced whale oil with an easily accessible, cheaper alternative; their husks were pulverized into fertilizer, reducing the nation’s dependence on imported Peruvian guano.

It was the beginning of large-scale industrial fishing. In Maine alone, more than twenty reduction plants dotted the shoreline, processing the largest, oiliest menhaden (the fish tend to migrate northward as they grow older). But by 1879, as Franklin has documented, menhaden had virtually disappeared from Maine waters, and were scarce along the entire New England coast. As northern factories were boarded up, Reedville became the beating heart of the menhaden reduction industry, with several factories clustered around Virginia’s Northern Neck, scooping up younger menhaden not far from their nursery in the Chesapeake Bay.

In the 1950s, the introduction of spotter planes and hydraulic technology to the fishery resulted in blowout years: 1.5 billion pounds of menhaden were caught in 1956, largely from the Chesapeake Bay and its environs. Ten years later, the catch had declined 70 percent, to 464 million pounds.

These harvest declines, combined with the newfound technological efficiency of the industry, wrought havoc on the culture of menhaden fishing and the landscape of the reduction business. The predominantly African American fishermen who once hauled in nets by hand, coordinating their efforts with a system of lyrical call-and-response, found themselves largely out of work. And the industry became heavily consolidated. By 1997, only two menhaden reduction facilities remained on the East Coast, and by 2005, Omega Protein owned the last factory standing. Over the years, every state along the Eastern Seaboard, with the exception of Virginia and North Carolina, has passed laws prohibiting the industrial reduction business from harvesting menhaden in state waters. But Omega Protein still has free rein where it counts. These days, from May to December, the company’s boats troll the Virginia waters of the Chesapeake Bay and the federal waters that stretch from three to 200 miles off the Maryland, Delaware, and New Jersey shores—the core areas where commercial-scale quantities of menhaden can still be found.

At every moment in this long history, the reduction industry has denied, counterintuitively, that fishing has any impact on the number of menhaden in the Atlantic. A publication of the United States Oil and Guano Association from 1884 asserted, “The plentitude or scarcity of sea fish is wholly independent of the operations of man, but is determined by the forces of nature.” To this day, Omega Protein maintains that menhaden have been subject to a historical pattern of ebbs and flows, driven by external factors like pollution and poor recruitment (the failure of young fish to enter the adult breeding population).

For most of the reduction industry’s history, these arguments didn’t need to carry much weight. Companies didn’t have to answer to regulators; they had only to contend with the occasional legislative annoyance brought on by the grievances of food fishermen and coastal residents who complained about the stink of menhaden smoke. Nobody was conducting stock assessments to determine how many menhaden were left. The prevailing attitude of the time was that there would always be fish in the sea. It wasn’t until 1981 that the ASMFC took responsibility for the little fish and, in the process, thrust itself into the path of a powerful industry.

Chartered by Congress in 1950, the ASMFC was meant to coordinate the management and conservation of migratory species in state waters. Initially this coordination was voluntary. The agency became much stronger with the passage of the Atlantic Coastal Fisheries Cooperative Management Act of 1993, which mandated that states comply with ASMFC decisions. The act also gave the secretary of commerce the ability to impose moratoriums on fisheries in states that were being obstreperous.

Today, the ASMFC is responsible for managing twenty-four species that swim, crawl, and scuttle between the shoreline and three miles out to sea, from the tip of Maine to the southernmost edge of Florida, where the Atlantic Ocean washes into the Gulf of Mexico. Every three months, politically appointed commissioners from fifteen Atlantic states and two federal agencies spend the better part of a week in windowless hotel conference rooms in coastal cities, arguing and occasionally coming to some tepid agreement about how to regulate striped bass, weakfish, American lobster, horseshoe crab, coastal shark, and forage fish like herring and Atlantic menhaden.

Science is the coin of the realm at the ASMFC. It’s the basis upon which regulatory battles are won and lost. Through testimony and fervent appeals, interest groups subtly manipulate fisheries science, leading to a constant “my science is better than your science” arms race. ASMFC meeting rooms are filled with non-scientist commissioners who begin their testimony with sentences like “Our science is not good,” or “We should delay action until we have better science.”

For the first twenty years, industry members had seats on the ASMFC’s menhaden committees, managing the very resource in which they had a financial stake. Nor was industry’s role purely administrative. Menhaden industry employees also sat on the science and statistical committees, ostensibly to assess the health and status of the menhaden population in the Atlantic. Meeting minutes from the 1980s and ’90s suggest, however, that industry members saw ASMFC meetings as opportunities to coordinate among themselves. At one meeting in 1983, in a possible indication that the industry was more worried about menhaden population levels than its public pronouncements suggested, representatives of Omega Protein, then called the Zapata Haynie Corporation, conferred with their competitors about shortening the fishing season and letting fish grow older and fatter before they were caught.

Company representatives remained on the menhaden management board until 2001, when conservation-minded regulators pointed out that menhaden was the only species managed by the ASMFC that openly enabled stakeholder votes on regulatory decisions. The industry representatives were kicked out in a close vote. But Omega continues to cast a long shadow over the ASMFC’s activities. In 2009, John V. O’Shea, ASMFC’s executive director, appeared in a promotional video for the company. He traveled to Omega’s corporate headquarters in Houston on the government’s dime, and stuck fairly close to a script provided by company executives, according to e-mails obtained through a public records request. The video remains on Omega Protein’s Web site, under their “Sustainability” tab, despite the fact that the arguments O’Shea articulated have since been contradicted by his own agency’s science. O’Shea has acknowledged that it was a poor idea to make the video.

Today, from grade school onward, students are taught in biology class to think of ocean ecosystems as webs of interdependence. Marine mammals eat big fish, big fish eat little fish, little fish filter particles like zooplankton and phytoplankton out of the water and convert plankton into a usable form of energy for big fish so they’ll be able to swim around and find little fish to eat. One of nature’s great dramas is its ruthless consumption of itself. The ASMFC’s fishery management plans, however, do not take account of the vast interconnectedness of ocean life. Rather, the agency is guided by an older and more utilitarian doctrine that is commonly characterized as “single-species management,” in which the primary concern is to determine how much of a particular species can be removed from the ocean without undermining that species’s ability to reproduce.

Single-species management is “an aggressive killing strategy,” says Ken Stump, a fisheries policy expert who has tracked marine science and management issues for the Marine Fish Conservation Network and Greenpeace. “It is premised on the assumption that you can remove 50 to 80 percent of an animal population and maintain high productivity, while you are fishing down a population to an incredibly low level.”

For menhaden, that level is set via a dizzying process that begins with the catch information logged by Omega’s ship captains and data gathered by the NOAA agent in Reedville. Those numbers are combined with several other data streams and then run through a computer model that takes into account historical information about the number of eggs that spawning females tend to produce and what proportion of menhaden tend to be killed by predators and fishermen. From all that, the model generates an estimate of the current “spawning potential” of adult female menhaden in the Atlantic, or the number of eggs they are capable of producing.

This estimate then goes before the ASMFC Menhaden Technical Committee, which is made up of NOAA scientists and biologists from state fisheries agencies. Their job is to weigh the menhaden’s current spawning potential against an estimate of how many eggs menhaden would produce in an imaginary world with no fishermen. The ratio of these two figures is called “maximum spawning potential.”

It is from these estimates that the committee derives the real magic number: the threshold below which the menhaden population would be unable to replenish or sustain itself. This threshold, which is debated and then voted on by the full commission, is called a “reference point.” The reference point currently in use for menhaden is 8 percent of maximum spawning potential. That is to say: according to the ASMFC, the Atlantic menhaden population can safely be fished down to 8 percent of the spawning potential that it would possess in a natural state.

This 8 percent level suits the reduction industry just fine, because it leaves plenty of headroom in the amount of fish it can extract from the ocean every year. But what remains behind in the water is an insanely small population from an ecological point of view. And it is far from ideal if you’re a recreational angler who fishes for striped bass, bluefish, or weakfish—the holy trinity of game fish on the Eastern Seaboard, all of which prey on menhaden. For anglers, the health of Atlantic predator fish is inextricably linked to the size and availability of menhaden in the ecosystem. Fishery managers may not be required to consider the ways in which ocean life is linked, but fishermen are keenly aware of the dynamics of the system.

And so, for decades, representatives from sport-fishing groups like the Coastal Conservation Association have descended on ASMFC meetings to lobby commissioners about changing the reference point and letting the menhaden population grow. Since the mid-1990s they have been joined by environmentally minded groups, including the National Coalition for Marine Conservation and the Chesapeake Bay Foundation, which came early to an understanding of the role forage fish play in maintaining the broader Atlantic ecosystem. But they have been no match for the lobbyists from Omega Protein. Until recently, they could do little to change the internal and industry-friendly logic that guided the setting of the ASMFC’s regulations.

One of the anglers who typically showed up at ASMFC meetings to bend the ears of commissioners was Jim Price, who began his solitary study of striped bass carcasses in 1997. On occasion, Price would also go fishing with a marine biologist he knew from the Maryland Department of Natural Resources, a burly guy by the name of Jim Uphoff.

Uphoff runs the Fisheries Habitat and Ecosystem Programs for the state of Maryland. In the late ’90s, he was working in and around the Chesapeake Bay as it was facing an incipient environmental disaster:striped bass from the estuary and its rivers were showing up with oozing red lesions on their flesh, and fishermen were demanding answers from the Maryland Department of Natural Resources. Uphoff was party to his fishing buddy Jim Price’s theory about the cause of this outbreak—that a growing striped bass population plus declining menhaden stocks left the stripers hungry, malnourished, weak, and chomping on other marine creatures that weren’t optimal sources of energy.

Uphoff was skeptical at first—afflicted, he admits, with a mentality common to fishery managers: “How can you have a problem finding food? The ocean is so big.” But new discoveries in bioenergetics, the study of how fish process energy from different food sources, eventually convinced him to take Price’s theories more seriously.

Looking harder into the ASMFC’s data, he noticed two things. First, the spawning potential “reference point” that the ASMFC set for menhaden was low compared to that of many other fish. Striped bass, for example, were only allowed to be fished down to 35 percent of maximum spawning potential. Second, the model the Menhaden Technical Committee used to derive the spawning potential estimate seemed overly complex and heavily dependent on industry-supplied data. So he devised a model that was simpler and could account for the impact of various predators on the menhaden stock.

In 2003, Uphoff went down to the NOAA lab in Beaufort to present his alternative in front of the scientists who had designed the one currently in use. When he ran his model, it showed that overfishing was occurring. The NOAA scientists, he says, were unimpressed. “Basically I was dead in the water in five minutes,” he recalls.

Meanwhile, interest in the menhaden problem was building among national environmental groups, many of whom learned about it from a 2001 article in Discover magazine by Rutgers historian H. Bruce Franklin. (Franklin was an avid angler himself and knew of Jim Price’s work.) By 2004, a coalition of anglers and environmentalists were demanding that the ASMFC adopt a harvest cap on menhaden fished from the Chesapeake Bay. The effort got some publicity in July 2005, when Greenpeace activists kayaked out to Cockrell Creek in front of Omega Protein’s Reedville factory and unfurled a splashy yellow banner that read “Factory Fishing is Overkill.”

In a vote later that year, the ASMFC agreed to implement a harvest cap. But the cap amount was calculated based on the average harvest from Omega Protein’s previous five years of fishing in the Chesapeake Bay. In other words, Omega wouldn’t sacrifice a single fish. Coalition leaders considered it to be the best they could get at the time—at least there was a check on the company’s activities for the first time in history. But others in the conservation community were not so happy. Tom Fote, an ASMFC commissioner from New Jersey and an ally of conservation, called it an “imaginary cap.”

Even an imaginary cap, it turned out, was too much for Virginia. In January 2006, Bob McDonnell, in his first month as Virginia’s newly elected attorney general, wrote a legal brief explaining that Virginia was not mandated to comply with the ASMFC’s decision. Documents I obtained show that this brief was based on a paper written by Shaun Gehan, then of Collier Shannon Scott, a law firm representing Omega Protein at the time. The state ultimately ended up complying the following year after a series of negotiations between Omega Protein, the ASMFC, and the state legislature.

While the ASMFC has proved itself deeply resistant to any action that might seriously affect Omega’s bottom line, it has also shown itself capable, at times, of making the sort of tough policy decision that can change the Atlantic marine world for the better. In 1982, the population of striped bass declined to fewer than 5 million fish. Overfishing and habitat degradation were threatening the existence of the species. The state of Maryland issued a five-year moratorium on striped bass fishing, turning the nursery and spawning-ground waters of the Chesapeake Bay into a kind of striper sanctuary. Soon, through the coordinated efforts of the ASMFC, the rest of the Atlantic states followed suit. Within a few years, the population came roaring back.

In 2007, there were 56 million stripers swimming around the Atlantic and its estuaries, gobbling up crabs, herring, and, of course, menhaden. Ecologists and anglers see this as a great success story and an argument for a more ecologically minded strategy of resource management. The reduction industry and its allies see things differently. One of Omega Protein’s closed-door arguments to the ASMFC was that anglers should be allowed to fish down the striped bass population, as that would remove a major competitor for menhaden, leaving more fish in the water for Omega Protein to catch.

Each year, Omega Protein scoops up between a quarter and a half a billion pounds of menhaden—as much as all of the ninety-nine factories that were operating in 1876 combined. More than half of Omega Protein’s sales come from exports abroad, with Asia and Europe representing the largest markets in a growing international aquaculture industry. Because it can take up to seven pounds of fish meal for a farmed specimen like salmon to put on one pound of body weight, Omega is capitalizing on a business model whereby menhaden are extracted from a wild ecosystem to fuel a much less efficient artificial one.

This vast protein extraction machine supports surprisingly few American jobs. A 2010 study by the economist James Kirkley at the Virginia Institute of Marine Resources found that the reduction industry has an $88 million economic impact on the Chesapeake Bay region, supplying 300 jobs at Omega Protein during the peak fishing season and 219 jobs in ancillary industries supported by the fishery. Recreational fishing, by comparison, has a $332 million economic impact in Virginia and Maryland, supporting 3,500 jobs, from bait and tackle shops to manufacturers of fishing equipment to charter-boat owners and captains—all of whom have an indirect stake in the health of the menhaden population.

Another industry with a significant economic stake in menhaden is the commercial lobster business, which uses menhaden as bait. In New England, decades of fishing pressure on sea herring, the preferred bait fish for lobster traps, have left the stock in precarious shape. Unable to purchase enough cheap herring to fill their traps, many lobstermen have turned to menhaden, lobster’s second-favorite food. In 2006, menhaden made up just 6 percent of lobster bait in Maine. Today it could be as high as 32 percent, according to the Fishermen’s Voice, a publication serving the men and women who work on Maine’s waters. Supplying those lobstermen is a bait industry that fishes primarily off the New Jersey and Virginia shores. Bait fishermen pull far fewer menhaden out of the sea than Omega Protein does, but those fish are worth more, pound for pound: bait commands a higher price per fish. In addition, the industry’s economic impact is spread among several different players and states.

All these stakeholder industries together have a massive economic footprint. And yet, precisely because it is dominated by a single, powerful entity, the reduction industry has held by far the greatest political sway over the management decisions of the ASMFC. This state of affairs is helped along by the fact that the bait and reduction industries have formed an unlikely alliance against any sort of regulation that might inhibit their catch—despite their being in competition for limited supplies of menhaden. This alliance is historically strange. In the nineteenth century, bait fishermen rioted and burned down at least one reduction factory in Maine, in response to the reduction industry’s massive sweep of the resource. “Now there’s no memory of this at all,” Bruce Franklin told me. “Omega has convinced the bait fishery that an attack on one is an attack on all. But in fact, the bait fishery is being allowed to fish from Omega’s crumbs that fall off the table.”

Recreational anglers, by contrast, are some of the most passionate advocates for the conservation of menhaden—or bunker, as the fish is known in New England. Anglers don’t harvest much of the resource themselves—the ASMFC estimates less than 1 percent of the total catch—but they know that where menhaden go, so go stripers, bluefish, weakfish, and dozens of other fish species they like to catch and eat. It is not uncommon, when scanning the popular angler message boards online, to see messages like “Last night Stripers were going berserk over juvy bunker!”

Throughout the 2000s, marine biologists continued to report diseased, scrawny striped bass in the Chesapeake Bay, the spawning ground for 75 percent of the Atlantic migratory population. In 2006, official ASMFC science showed depleted stocks of weakfish as well. The reason: with low numbers of menhaden, striped bass were out-competing weakfish for prey, and increasingly munching on weakfish juveniles to make up for lost calories. That study came on the heels of another on ospreys, which feed heavily on menhaden in Virginia. According to decades of research by the College of William and Mary’s Center for Conservation Biology, by 2006 osprey parents were bringing one-third fewer fish back to their chicks than they were in the 1970s. Survival of osprey nestlings in Virginia had fallen to its lowest levels since DDT was first introduced to the area. In the 1980s, more than 70 percent of the osprey diet was menhaden; by 2006 it was down to 27 percent.

Yet despite the steady drip of evidence, and continued lobbying by angler and environmental groups, the ASMFC took no action to limit the coastal menhaden catch in the mid-2000s. When pressed, commissioners would point to the stock assessments, which continued to show that the menhaden population was relatively healthy and not overfished.

In 2009, the Menhaden Technical Committee updated its methodology for estimating the menhaden population—something it does every five years—and then ran the menhaden catch data through a new computer model. The results weren’t much different: although the numbers of menhaden were declining, the estimated number of eggs produced by spawning female menhaden was at the target level, so according to the reference point, menhaden weren’t being overfished.

Shortly thereafter, a colleague of Jim Uphoff’s, a biologist named Alexei Sharov, got hold of the computer model that had been updated by NOAA scientists. Going through the code line by line, Sharov, one of Maryland’s representatives on the Technical Committee, found a fundamental miscalculation buried inside the model. Uphoff, meanwhile, studied the methodology of the code and discovered that NOAA had both underestimated the amount of fish killed by the industry and overestimated the spawning potential. Sharov brought these two mistakes to his peers on the committee, and it was agreed that corrections needed to be made.

Several months later, after the model had finished running a second time, the science finally caught up with what Jim Price and the anglers had been saying for decades: even using the lax reference points developed by the ASMFC, menhaden had been subject to overfishing in thirty-two of the past fifty-four years. When the assessment was then peer reviewed by a group of international scientists, the reviewers deemed that the reference point currently in use for menhaden—8 percent of maximum spawning potential—was not sufficiently safe or precautionary.

Furthermore, the number of menhaden swimming in the Atlantic had declined by 88 percent since 1983—to a level so low that it caused George Lapointe, former commissioner of Maine’s Department of Marine Resources, to have what he called an “oh shit moment.”

Five months later, in August 2011, the ASMFC reviewed its menhaden stock assessment and, in the fashion of twelve-step programs, begrudgingly admitted that it had a problem. They prepared a long and technical document to send out for public comment. At the heart of it was the question of how big the base population of menhaden should be, as expressed in terms of spawning potential. The document listed four options. The lowest was the number ASMFC had long recommended: 8 percent of maximum spawning potential, or MSP. The highest option was 40 percent of MSP. Even that was far below what independent scientists have advised in recent years. A 2011 paper published in the journal Science recommended precautionary management for forage fish, leaving up to 75 percent of virgin biomass in the water to account for the needs of predators. Still, the range of options represented a major advance. Of the 91,000 comments the ASMFC received on the proposal over the next three months, the majority argued for 40 percent.

The meeting to vote on the proposal took place in Boston on an unseasonably warm day in November 2011. Anglers came from far and wide—Maine, Rhode Island, Virginia, North Carolina—wearing olive and gray caps with embroidered striped bass and buttons that said “Save the Bunker” and “Save Menhaden Now.” Many drove in on so-called Bunker Buses, arranged jointly by sport-fishing clubs and environmental organizations. Paul Eidman, an angler from New Jersey who founded the group Menhaden Defenders, towed a billboard in his truck that depicted a striped bass made up of tiny, swimming menhaden. “No Bunker, no Bass,” the sign read, drawing cheers as it was installed outside the ASMFC meeting room. Whale watchers came from Maine, charter-boat owners from Maryland, commercial bait fishermen from New Jersey and Virginia, and environmentalists from the Chesapeake Bay region. Omega Protein’s senior scientist, public relations director, and plant manager sat together in the middle of the audience, looking glum.

As soon as the meeting began, it became clear that for the commissioners, the 40 percent figure was too radical a change. The opening bid was for a 30 percent limit. The question was how much lower it would go, and there were political currents below the surface pulling for the lowest possible number. In advance of the meeting, Virginia Governor McDonnell had approached five Republican governors along the coast, urging them to join him in choosing an option that would be less damaging to the reduction fishery. The night before the meeting, New Jersey Governor Chris Christie had called his commissioners and instructed them to vote with Virginia. New Jersey is home to Lund’s Fisheries, the largest menhaden bait company on the Eastern Seaboard, employing eighty-five fishermen.

In the end, it didn’t matter. New Jersey and Virginia were the only states to vote against setting the new reference point at 30 percent of MSP. After the vote, a grateful audience burst into applause. At least one conservation-oriented commissioner began to cry. For many, the vote was twenty years in the making.

Jim Price was not at the meeting that day. He was out in his boat on the Choptank River with Jim Uphoff and another scientist. But Price had his iPad with him and followed the vote in real time via Twitter. He smiled quietly when he read the news. “It changed the mood on the boat that day,” he told me.

That night, Omega Protein’s stock plummeted from nearly $11 per share to $8.54, and ultimately lost 35 percent of its value in a nine-day period. Six months later, the stock has barely recovered.

While the new reference points are a major breakthrough, the effort to protect the menhaden is by no means a done deal. Omega Protein may pursue any of three different strategies to protect its market share and foil conservationists’ hopes.

The first option is to delay rollout of the new rule. This past winter the ASMFC, ever the cautious body, put out a document asking for public comment on the appropriate timeline for implementing its new 30 percent preservation rule. Options include one, three, five, or ten years. (The ten-year time frame was not originally on the table, but Jack Travelstead, an ASMFC commissioner from Virginia, lobbied to have it included.) Ten years would buy Omega lobbyists the time they need to work the Menhaden Technical Committee and secure higher catch limits. In a call to investors and stock analysts in March, Omega CEO Brett Scholtes said the company viewed the ten-year timeline as “directionally favorable.”

Omega’s second option is simply to send its ships farther out into the ocean. The ASMFC only regulates state waters between the shore and three miles out to sea—which is traditionally where most menhaden fishing has taken place. The territory between three and 200 nautical miles is called the Exclusive Economic Zone (EEZ), and is subject to fairly loose federal monitoring under the jurisdiction of NOAA. “What goes on in the EEZ is still the wild west. There’s little oversight and enforcement, so we are relying entirely on the honesty of people at the dock, fish-processing companies, or wholesalers that buy the fish and put it out to market,” says Paul Eidman, founder of Menhaden Defenders.

The company’s third option—a nuclear option, really—is to convince Virginia politicians to secede from the ASMFC. The ASMFC is a voluntary compact between states, and Virginia nearly left it once before, in 1996, objecting to the constitutionality of a congressional mandate that states comply with regulations put in place by the ASMFC. That secession bill passed both the Virginia House and Senate and was even signed into law by then Governor George Allen before ultimately being scrapped when the legislature took it up again the following year.

As reductions to Omega Protein’s harvest loom, Virginia State Senator Richard Stuart has introduced a bill that would withdraw Virginia from the ASMFC entirely, a move that would affect not only menhaden, but every other marine species, fishermen, and maritime industry in the Old Dominion State, the nation’s fourth-largest seafood provider.

“I drafted my bill to demonstrate to the ASMFC that Virginia will not tolerate ignoring the best available data on menhaden,” Stuart told a reporter. His bill was referred to committee, and has been carried over to the 2013 legislative session. If it passes, as some suspect it might, Governor McDonnell will have an opportunity to sign it before he leaves office in early 2014 (presuming, of course, that he does not become part of a successful Romney ticket this year).

Presumably, for Virginia, withdrawing from the ASMFC would be a prelude to disregarding its rules. If Virginia does ignore the ASMFC’s menhaden regulations, the commission would have no choice but to find the state “out of compliance.” Unless Virginia changed its tune, the case would go to the U.S. secretary of commerce, who would have the authority to shut down the menhaden fishery altogether if negotiations failed to resolve the issue. Because of all the mandatory delays and timetables involved, the process could drag on for months or years, only to end in an eleventh-hour compromise. For Omega Protein, it could be the ultimate delay game, allowing the company to fish to its heart’s content while it waits for more favorable science and continues lobbying.

But there is another possible scenario, one even more dire. If Virginia refuses to comply with the secretary of commerce, the matter could end up in federal court. This would not only entail further delays, with the possibility of a lengthy appeals process; at a time when constitutional arguments for states’ rights are gaining traction, this disagreement over the lowly menhaden could be grounds for questioning the constitutionality of the federal government’s power to interfere with the state of Virginia and its ability to manage its own natural resources.

And yet, for all the cards Omega might play to avoid regulation, its most historically important weapon—the ASMFC “science” that once supported its claims to menhaden—has now become a huge liability. The company’s business model is also being challenged, as scientists around the globe race to develop vegetarian fish feed to reduce pressure on wild forage fish used in fish meal. More and more, the whole forage fish reduction industry is looking like an anachronism. A report released in April by the Lenfest Forage Fish Task Force, managed by the Pew Charitable Trusts, estimated that the value of leaving forage fish in the ocean as a food source for predators is $11 billion—twice as much as the $5.6 billion those fish generate when reduced into fish meal and fish oil for things like aquaculture, farming, human supplements, and pet food.

Stepping back from the sprawling scope and maddening complexity of the menhaden story, there’s a near-comical aspect to the image of this silvery fish, darting around in a pail of briny water or frozen in a carton of bait, confounding the American system of governance. It’s hard to fathom that something as seemingly simple as regulating the catch of a bunch of oily fish could be so spectacularly elusive, or that this tiny creature could be so crucial to the ecological balance of the oceans and the health and well-being of life on land. At some point, economic logic and political pressure will probably force Omega Protein out of the menhaden fishing business. The question is how much damage this one company will do to the ocean’s ecology in the meantime.