AUGUSTA, Maine — Given colonial-era history between Maine’s Native Americans and European settlers, it would be reckless to say that relations between the tribes and the state are at an all-time low but there’s no question that problems of historic proportions exist.

In May 2015, two of Maine’s four tribes withdrew their representatives from the Legislature after a years of clashes, culminating with Gov. Paul LePage’s cancellation of his own four-year-old executive order in April 2015 that said the tribes would be consulted on state decisions that affect them.

On that sunny May morning, the Passamaquoddy and Penobscot tribal’ representatives made brief speeches and walked out of the House to join hundreds of tribal members gathered outside. The two tribes severed their relationship with the legislative branch in what unquestionably was a stunning development after almost two centuries of sending envoys to Augusta.

“We have gotten on our knees for the last time,” Kirk Francis, chief of the Penobscot Nation, said on that historic day. “From here on out, we are a self-governing organization focused on a self-determining path.”

The clashes have continued since then in court, at the State House and on Thursday afternoon in the Legislature’s Judiciary Committee, where the tribal chiefs and dozens of their people filled two overflow rooms for the presentation of another report that the tribes say proves their reservations are sovereign nations within U.S. borders. The exchange grew heated when Rep. Stacey Guerin, R-Glenburn, asked about state funding for the Maine Indian Tribal-State Commission, which was presenting the report.

“If MITSC gets $30,000 from the state of Maine, I’m sure all of these tribes sitting here and all these people sitting here will take it out of their pockets and give it to them themselves,” said William Nicholas, co-chief of the Passamaquoddy Tribe at Indian Township, pausing as the rooms erupted in applause. “I feel a little bit offended that we’re being asked about money today when there’s a whole book in front of you that outlines the problems we’re facing with the state. … It brings us to a point where questions like that make us feel like we’re about this big,” he said, holding two fingers inches apart.

What has gone so wrong?

Fights about sovereignty for Maine’s tribes date back decades. The U.S. Department of Justice filed a $150 million suit against the state of Maine on behalf of the Passamaquoddy Tribe in the early 1970s, a claim that quickly ballooned to billions of dollars when the Penobscot Nation filed a similar complaint. Years of negotiations led to settling the matter — or so it thought — in 1980 with passage of the Maine Indian Claims Settlement Act.

The tribes argue that an eleventh-hour amendment inserted into the act without their knowledge — “Section 1735(a)” — foiled their sovereignty and left their hands tied on issues ranging from hunting and fishing rights to fighting drugs and crime to declaring natural disasters on their own reservations. The tribes’ position is that some courts have interpreted this section incorrectly.

Since 1980, tribal leaders have argued that Section 1735(a) legally institutionalizes second-class status for Maine’s tribes, depriving them of equal footing in negotiations and creating bureaucratic loopholes that prejudice state and federal courts and agencies against them.

In recent years, there have been fights over casino revenue and the tribes always lose. Perhaps the most public of those clashes has been the years-long conflict over whether to allow the tribes to operate casinos. In their efforts to emulate tribes in other states that opened casinos, some of whom reaped huge windfalls from doing so, Maine’s tribes have been shut out after voters rejected tribal-backed casino referendum campaigns in 2003 and 2007. Legislative forays dating back at least to 1992 have sputtered, including bills that failed by slim margins in 2014 and 2015.

Exacerbating those losses, the first casino in Maine, Hollywood Slots in Bangor, devastated the revenue stream to the Penobscot Nation’s bingo hall on Indian Island, according to tribal leaders. Groups and locals who used to travel to the bingo hall instead started going to the nearby casino, cutting a major revenue stream to the tribe to a trickle.

There have been new legal clashes. The Penobscot Nation sued the state in 2012 over hunting and fishing rights along the Penobscot River. The tribe essentially lost the case in 2015 when a federal judge ruled that the Penobscots can claim guaranteed sustenance fishing rights, but no exclusive rights to the waters around Indian Island and other islands that are part of the reservation.

An April 2016 appeal of that ruling by the tribes is pending in the 1st U.S. Circuit Court of Appeal in Boston. The Penobscot Nation is also fighting for higher water quality standards that some municipalities have argued could cost them millions of dollars. The U.S. Environmental Protection Agency sided with the tribe with new water quality standards issued late last year, but a lawsuit brought by the Maine Department of Environmental Protection in 2014 remains pending in U.S. District Court in Bangor.

The Passamaquoddy Tribe has been waging a separate years-long battle against the state over tribal access to the lucrative Down East elver fishery. Tribal members have argued that the state’s enforcement of regulations that state officials said were designed to preserve the fishery effectively blocked the tribes from capitalizing on soaring global prices.

In 2013, tribal members poured into the State House to express their concerns, again arguing that development and regulation encouraged by the state undercut their traditional way of life.

“I don’t see how hydroelectric dams can chew up thousands and thousands of egg-bearing eels, and the Passamaquoddy can’t take some to feed their family,” said Fred Moore III, then Fishery Committee coordinator for the Passamaquoddy Tribe.

It hasn’t gone well for the tribes at the State House. In 2015, LePage rescinded his prior executive order, reversing the creation of special communication channels between the state and the Passamaquoddy Tribe, the Penobscot Nation, the Houlton Band of Maliseets and the Aroostook Band of Micmacs. The tribes saw it as retribution for the fight over water quality.

There have been a slew of bills aimed at granting the tribes special powers on a range of issues, including one in 2015 that would have allowed for the creation of tribal courts to prosecute non-Indian offenders when they commit certain domestic violence and sexual assault crimes. The bill died when the 127th Legislature adjourned without acting on it.

The Penobscots will not return to the Legislature anytime soon. Chief Francis said his tribe has decided recently to create ambassadors to federal and state governments, who will be named soon. He said the push at the federal level will be to convince Congress that Maine isn’t abiding by the settlement act. In Maine, it’s social issues that will be the focus.

“This is not a gaming issue anymore,” he said. “We’re talking about fishing. We’re talking about the ability to protect domestic violence victims. We’re talking about dealing with cancer rates that are three or four times higher than the general population. Heart conditions at five times higher. Diabetes in over 20 percent of our community. … This is about the core basic rights of the tribe that are under attack.”

Tribal sovereignty, even if it happened tomorrow, would be just the beginning of a fundamental change in how tribal leaders and virtually every level of government interact. With rights around property, gaming and natural resources at stake, the financial impacts on both the public and private sectors would be considerable. While the conflict on the surface appears to be about civil rights and a legal or political compromise, underlying financial factors likely worth millions of dollars can’t be ignored.

Christopher Cousins has worked as a journalist in Maine for more than 15 years and covered state government for numerous media organizations before joining the Bangor Daily News in 2009.