Opposing parties in the legal battle over mercury pollution from the former HoltraChem plant late this week filed two different plans in federal court in Portland describing how the lower Penobscot River should be cleaned up.

In 2000, the Maine People’s Alliance and the Natural Resources Defense Council filed a civil lawsuit to force Mallinckrodt Inc. to study how mercury from the Orrington chemical plant has affected ecosystems downriver from the site.

Mallinckrodt, which owned the plant for 15 years until 1982, had agreed previously to take responsibility only for the plant itself and a small section of the Penobscot just south of the site.

In July, a federal judge ordered Mallinckrodt to pay for a broader study of how mercury pollution has affected the Penobscot River. The company was told to work with the MPA and NRDC in drafting a plan for scientific research, and to submit it to the court by Friday.

Instead, two plans were filed by the plaintiffs and defendants.

“There was a legitimate effort to work together,” said John Dieffenbacher-Krall, co-director of the MPA. “What we have found is that Mallinckrodt has constantly preferred to fight than to clean up the river.”

On Thursday, the Maine People’s Alliance submitted a 25-page plan that calls for at least three years of scientific study at a cost of between $1 million and $3 million.

Although the extensive research will delay any cleanup of the river, the work is necessary to determine the full extent of the damage that mercury pollution has caused, Dieffenbacher-Krall said Friday.

“There is no organization more anxious for cleanup than the Maine People’s Alliance, but it’s important that the questions are answered properly,” he said. “This is a dynamic ecosystem. It’s not like adding one plus one equals two.”

MPA’s plan calls for two years of field research to be conducted throughout the Penobscot River estuary into “mid-Penobscot Bay.” Research would include such projects as sediment sampling, a range of plant and wildlife studies, and water flow models tracing how pollutants might move through the system.

Scientists then would spend a year and a half analyzing the data and proposing remedies, if necessary.

Mallinckrodt filed its own plan late Friday afternoon, according to a court clerk in Portland. A Mallinckrodt spokesperson did not return calls seeking comment Friday, and did not make a copy of the plan available to the newspaper.

Later this year, U.S. District Court Judge Gene Carter, who issued the original ruling, is expected to decide what the actual river study will include. A decision is expected by the end of the year, and scientific research is set to begin next spring, said Dieffenbacher-Krall.

“Finally, we’ll have some real science done. We’ll have the answers that people want to know,” he said.

On Wednesday, Mallinckrodt appealed the judge’s original order that it fund a Penobscot River study, and asked both the U.S. District Court in Portland and the 1st Circuit Court of Appeals in Boston for an extension so that it would not have to file a plan this week. Both courts denied the extension Friday. The appeal is still pending.