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The scene at McNiff Farm in December

AYER — Life was not good for “a Jersey with a yellow tag ‘Mickey.'” It was even worse for piglet #845 with a broken rear leg and the red heifer with a severe case of ringworm.

They were among the 185 swine, 14 cattle and various sheep and goats confined to a five-acre property in Ayer.

Dead animals and inches of mud and manure were the companions of the livestock. Some were thin; others were very thin. Some had diarrhea. Some were thirsty or had conjunctivitis or an abscess.

Rats roamed the yard and barns.

Five free-ranging ducks seemed to be just fine.

Reports and documents from the Massachusetts Department of Agricultural Resources, MDAR, detail the conditions found in November at the home and farm belonging to Ralph McNiff. Some animals belonged to him and the rest were owned by his son Troy McNiff.

The farm got what looked like a clean bill of health during a Nov. 3, 2016 state inspection of the garbage treatment. The federal Swine Health Protection Act governs what swine can be fed in order to protect public health.

All of the correct boxes were checked by the state inspector, just like in the reports from previous inspections dating back to 2013.

* “Health of all animal species.” Satisfactory. According to the reports the animals appeared healthy and free of obvious signs of infectious or contagious disease.

* “Pest control.” Satisfactory. There was no obvious evidence that either rats or flies infested the property because of the way feed was stored.

There was one difference on that early November 2016 report. A handwritten note at the bottom said, “Cook test scheduled for 12/1.”

According to a narrative report written in December by the inspector, Jessica Edwards, the shelter for the animals was not acceptable. It would not protect the animals in cold weather and there was not enough space for all of them to take cover. She arranged to come back in December to test the garbage cooker.

Instead, she returned on Nov. 23 for a surprise inspection, now with an MDAR animal inspector and a Massachusetts Society for the Prevention of Cruelty to Animals officer. Conditions were worse than a substandard shelter noted during her earlier visit.

A strong odor came from an area where Troy kept his 83 swine. Those pigs were eating the carcasses of other pigs. Inspectors counted nine dead and decaying bodies and other remains.

Troy said his wife had told him there were dead pigs.

Rats ran over the rafters. Inspectors saw rat tunnels.

The livestock that had bedding, not all of them did, were itchy. Ralph told the inspectors that his son Troy was using recycled sawdust that had lice from chickens.

Cattle roamed land littered with abandoned vehicles and debris with sharp edges.

Ten calves, nine goats and nine sheep were penned together. Troy told inspectors “that he feeds everyone the same food at the same time.”

Some of that food was toxic to the sheep. Some of the feed was medicated. The treatments and medications given to the animals was not clear.

Troy said he did not feed the animals on a particular schedule.

While the inspectors were there, a pickup truck dropped off pineapples and melons for Troy’s pigs. The pen was so crowded that some pigs could not get to the fruit.

Troy became aggravated when talking with the inspectors, the report said. Then, he agreed with everything that was asked of him and said he was 100 percent at fault.

The MSPCA officer told Troy the pigs had to leave the farm immediately. Eight in the poorest health, including the piglet with the broken leg, were sent on a trailer to be rendered at Blood Farm in Groton.

Others were sent, under quarantine, to FLAME, the Farmers Livestock Auction and Market Exchange in Littleton. They would be cared for there until they could be killed after Thanksgiving.

Three died in Littleton over the weekend, despite having food, water and shelter.

Over the next few days, Troy continued to move animals away from the farm. It did not go smoothly.

Inspectors followed him to Blood’s in Groton. The trailer he was hauling with seven pigs tipped over. A sow walked off down the road.

The Groton Animal Control Officer and both Ayer and Groton Police Departments showed up to assist in moving the six remaining animals to a borrowed trailer.

The sow remained missing that Friday, Nov. 25.

The McNiffs found the sow and shot her, bringing the body back to the farm. The Groton animal control officer left that information in a message to the MDAR inspector on Sunday.

On Nov. 28, eight calves, some too small to reach the drinking water, remained on the farm. Four sows and one boar left for Adams Farm Slaughter House in Athol. The dead swine were still in Ayer.

On Nov. 30, two of the 48 swine moved to Hilltown Pork in New York died during the night.

The last animals were removed from the Ayer property in mid-December.

Inspectors kept track of the animals that could never be used for human consumption.

The McNiff family ran afoul of local inspections in the past. In 2008, the Board of Health and the Zoning Enforcement Officer played hot potato with responsibility for overseeing the farm.

At question, according to newspaper articles included in the state documents, was how to deal with the number of unregistered vehicles on the property.

The Board of Health said it was a zoning problem. The Zoning officer said the land had a “non-conforming” use and would be under the jurisdiction of the Board of Health.

The outcome is not clear, but Ralph McNiff was supposed to submit a plan of action to the town.

In November 2016, after the arrival of the MSPCA and MDAR, the town got involved.

The Ayer animal inspector investigated and filed a report on Dec. 6. “On a personal note: I, as Animal Inspector for the Town of Ayer, am deeply saddened to see the deterioration and decline of this farm,” Carlene Purdy wrote at the end of her formal report.

The Police Department started an investigation and Troy McNiff faces a trial in Middlesex Superior Court on animal cruelty charges.

The town got a court order that allowed it to clean up the site. Exterminators spent over a month visiting daily and continue to monitor for rats.

The house was condemned. It and most of the outbuildings were torn down. Abandoned vehicles are gone.

In February the Middlesex Superior Court granted an order allowing the town to remove the buildings and harborage. The work should be complete by mid-March, Town Administrator Robert Pontbriand wrote in an email.

The court authorized the town to place liens on the property for expenses. The bill, on Feb. 1, stood at $114,610.38, Pontbriand said. There will be further costs.

As of January, McNiff owed just under $25,000 in back taxes on the property.

In addition to sending the report and other materials after a public records request, MDAR provided background information. Telephone numbers were redacted.

Not included were the annual reports by the Ayer animal inspector. The town records are confidential and are not subject to the public records law exemption, said a letter from Carol A. Szocik, the records officer for MDAR.

Follow Anne O’Connor on Twitter and Tout @a1oconnor.