BOSTON – Five stacks of documents covered the desk at John Pappalardo’s Chatham home, more than a dozen three-ring binders covered his floor and a week-old growth of beard covered his face.

Pappalardo, a member of the New England Fishery Management Council, begins three days of meetings Tuesday to determine the future of New England’s centuries-old fishing industry, and the mess he described this week was a product of his preparation.

Years of analysis, arguments and cutbacks precede the meetings, but their result is anyone’s guess.

“It’s a crossroads for the fish, and the fishermen,” said Pappalardo, a commercial hook fisherman.

The council is charged with choosing a slate of tough new fishing rules, called Amendment 13, which could include cuts in fishing days, strict quotas and area shutdowns.

The changes were ordered by U.S. District Judge Gladys Kessler, who ruled in December 2001 that the regulators weren’t doing enough to end overfishing, as required in the Sustainable Fisheries Act of 1996.

Amendment 13 goes into effect next May, and a council analysis projects 2,100 to 3,000 lost jobs in the first year alone, depending on what rules are ultimately implemented.

Environmentalists say the reward for the short term pain will be healthy fish populations on which fishermen can earn a robust living. But fisherman say the rules could force most out of business before they can enjoy any rebound, reducing New England’s coastal ports to relics of a lost way of life.

The months since Kessler’s ruling have seen sometimes angry debate about the need for the new rules, the science behind them and intentions of the players on various sides of the issue.

This week at the meetings in Peabody, the debate ends and all that matters is satisfying Kessler, whose court is in Washington, D.C.

Craig Pendleton, a 43-year-old fisherman based in Portland, said he’s already told his crew they might be out of work soon.

“This is the most worried I’ve ever been, as far as what the rules could do to me as a businessperson,” he said. “My entire career is in limbo right now.”

Geoff Smith of the Ocean Conservancy, an environmental group, sees the meetings as an opportunity to begin restoring a healthy fishery after years of ineffective half-measures by the council that made things worse. His group was one of four environmental groups that brought the lawsuit that resulted in Kessler’s ruling.

“It’s time for the council to step up and end overfishing,” Smith said.

The council is a regional advisory body to the federal National Marine Fisheries Service and its recommendations have generally been heeded by NMFS. But the council – which is made up of environmentalists, scientists and fishing industry representatives – risks losing that influence if it comes out of this week’s meeting with a plan federal regulators don’t think will pass legal muster.

The list of issues the council must address goes to the basics of fishery management – including what counts as a fishing day at sea and how to define when a species has been overfished.

Before them are five alternative plans, each of which will have been prescreened for legal soundness.

There have been questions leading up to the meeting about the basic ground rules for crafting Amendment 13. Pappalardo said he and other council members planned to “mix and match” pieces of the five alternatives, rather than pick one in its entirety.

He cited NMFS director William Hogarth, who advocated “flexibility and creativity” in achieving a “mix of measures” that would satisfy the law and also preserve fishing communities in an Oct. 2 letter to council Chairman David Borden.

In an interview Wednesday, Hogarth clarified his remarks, saying there likely was no time for the council to essentially create a sixth or seventh alternative by cobbling together pieces of the first five, and get that new alternative legally approved.

“I think it would be difficult,” he said. “I think they ought to tweak what they got.”

Pendleton said he has sympathy for the council and the pressure they face.

“You’re depending on 18 people from New England to decide the fate of over 1,400 permit holders,” he said.

Asked if he thought they could come up with rules that preserve both fish and fishermen, he was noncommittal.

“I’m hoping and praying they can,” he said.