The sheriff looked to the local militia to defend the court against these armed farmers. But most of the militia was with Luke Day. The sheriff did manage to gather five hundred men, and the judges put on their black silk robes, waiting for the sheriff to protect their trip to the courthouse. But there at the courthouse steps, Luke Day stood with a petition, asserting the people's constitutional right to protest the unconstitutional acts of the General Court, asking the judges to adjourn until the General Court could act on behalf of the farmers. Standing with Luke Day were fifteen hundred armed farmers. The judges adjourned.

Shortly after, at courthouses in Worcester and Athol, farmers with guns prevented the courts from meeting to take away their property, and the militia were too sympathetic to the farmers, or too outnumbered, to act. In Concord, a fifty-year-old veteran of two wars, Job Shattuck, led a caravan of carts, wagons, horses, and oxen onto the town green, while a message was sent to the judges:

The voice of the People of this county is such that the court shall not enter this courthouse until such time as the People shall have redress of the grievances they labor under at the present.

A county convention then suggested the judges adjourn, which they did.

At Great Barrington, a militia of a thousand faced a square crowded with armed men and boys. But the militia was split in its opinion. When the chief justice suggested the militia divide, those in favor of the court's sitting to go on the right side of the road, and those against on the left, two hundred of the militia went to the right, eight hundred to the left, and the judges adjourned. Then the crowd went to the home of the chief justice, who agreed to sign a pledge that the court would not sit until the Massachusetts General Court met. The crowd went back to the square, broke open the county jail, and set free the debtors. The chief justice, a country doctor, said: "I have never heard anybody point out a better way to have their grievances redressed than the people have taken."

The governor and the political leaders of Massachusetts became alarmed. Samuel Adams, once looked on as a radical leader in Boston, now insisted people act within the law. He said "British emissaries" were stirring up the farmers. People in the town of Greenwich responded: You in Boston have the money, and we don't. And didn't you act illegally yourselves in the Revolution? The insurgents were now being called Regulators. Their emblem was a sprig of hemlock.

The problem went beyond Massachusetts. In Rhode Island, the debtors had taken over the legislature and were issuing paper money. In New Hampshire, several hundred men, in September of 1786, surrounded the legislature in Exeter, asking that taxes be returned and paper money issued; they dispersed only when military action was threatened.

Daniel Shays entered the scene in western Massachusetts. A poor farm hand when the revolution broke out, he joined the Continental army, fought at Lexington, Bunker Hill, and Saratoga, and was wounded in action. In 1780, not being paid, he resigned from the army, went home, and soon found himself in court for nonpayment of debts. He also saw what was happening to others: a sick woman, unable to pay, had her bed taken from under her.

What brought Shays fully into the situation was that on September 19, the Supreme Judicial Court of Massachusetts met in Worcester and indicted eleven leaders of the rebellion, including three of his friends, as "disorderly, riotous and seditious persons" who "unlawfully and by force of arms" prevented "the execution of justice and the laws of the commonwealth." The Supreme Judicial Court planned to meet again in Springfield a week later, and there was talk of Luke Day's being indicted.

Shays organized seven hundred armed farmers, most of them veterans of the war, and led them to Springfield. There they found a general with nine hundred soldiers and a cannon. Shays asked the general for permission to parade, which the general granted, so Shays and his men moved through the square, drums hanging and fifes blowing. As they marched, their ranks grew. Some of the militia joined, and reinforcements began coming in from the countryside. The judges postponed hearings for a day, then adjourned the court.

Now the General Court, meeting in Boston, was told by Governor James Bowdoin to "vindicate the insulted dignity of government." The recent rebels against England, secure in office, were calling for law and order. Sam Adams helped draw up a Riot Act, and a resolution suspending habeas corpus, to allow the authorities to keep people in jail without trial. At the same time, the legislature moved to make some concessions to the angry farmers, saying certain old taxes could now be paid in goods instead of money.

This didn't help. In Worcester, 160 insurgents appeared at the courthouse. The sheriff read the Riot Act. The insurgents said they would disperse only if the judges did. The sheriff shouted something about hanging. Someone came up behind him and put a sprig of hemlock in his hat. The judges left.

Confrontations between farmers and militia now multiplied. The winter snows began to interfere with the trips of farmers to the courthouses. When Shays began marching a thousand men into Boston, a blizzard forced them back, and one of his men froze to death.

An army came into the field, led by General Benjamin Lincoln, on money raised by Boston merchants. In an artillery duel, three rebels were killed. One soldier stepped in front of his own artillery piece and lost both arms. The winter grew worse. The rebels were outnumbered and on the run. Shays took refuge in Vermont, and his followers began to surrender. There were a few more deaths in battle, and then sporadic, disorganized, desperate acts of violence against authority: the burning of barns, the slaughter of a general's horses. One government soldier was killed in an eerie night-time collision of two sleighs.

Captured rebels were put on trial in Northampton and six were sentenced to death. A note was left at the door of the high sheriff of Pittsfidd:

I understand that there is a number of my countrymen condemned to the because they fought for justice. I pray have a care that you assist not in the execution of so horrid a crime, for by all that is above, he that condemns and he that executes shall share alike… — Prepare for death with speed, for your life or mine is short. When the woods are covered with leaves, I shall return and pay you a short visit.

Thirty-three more rebels were put on trial and six more condemned to death. Arguments took place over whether the hangings should go forward. General Lincoln urged mercy and a Commission of Clemency, but Samuel Adams said: "In monarchy the crime of treason may admit of being pardoned or lightly punished, but the man who dares rebel against the laws of a republic ought to suffer death." Several hangings followed; some of the condemned were pardoned. Shays, in Vermont, was pardoned in 1788 and returned to Massachusetts, where he died, poor and obscure, in 1825.

It was Thomas Jefferson, in France as ambassador at the time of Shays' Rebellion, who spoke of such uprisings as healthy for society. In a letter to a friend he wrote: "I hold it that a little rebellion now and then is a good thing… It is a medicine necessary for the sound health of government… God forbid that we should ever be twenty years without such a rebellion… The tree of liberty must be refreshed from time to time with the blood of patriots and tyrants. It is its natural manure."

But Jefferson was far from the scene. The political and economic elite of the country were not so tolerant. They worried that the example might spread. A veteran of Washington 's army, General Henry Knox, founded an organization of army veterans, "The Order of the Cincinnati," presumably (as one historian put it) "for the purpose of cherishing the heroic memories of the struggle in which they had taken part," but also, it seemed, to watch out for radicalism in the new country. Knox wrote to Washington in late 1786 about Shays' Rebellion, and in doing so expressed the thoughts of many of the wealthy and powerful leaders of the country: