On Monday, 24 October, Clement was part of a working party in the wood yard in Boston. The work party broke for dinner, their mid-day meal, at 1 o'clock in the afternoon and assembled again at 3. About a half hour after reassembling the party and directing them to stack wood, the serjeant commanding the party noticed that Nicholson was missing; another soldier said that Nicholson had complained of being unwell before the meal, so the serjeant assumed that to be the reason for his absence. When the work party was dismissed in the evening the serjeant went to a serjeant of Nicholson's company and inquired after him. The two serjeants asked around for Nicholson, and on not learning his whereabouts reported his absence to the captain of the company. They searched his knapsack and found two white shirts, one check shirt and a pair of stockings missing. The officer ordered them to search for Nicholson but they did not find him.
A little after seven that evening two officers of the 4th Regiment and a servant were in Charlestown, heading towards the ferry that would take them to Boston. About a mile from the ferry they came upon two soldiers heading rapidly in the other direction. When the officers spoke to them, the soldiers appeared confused, so one officer took hold of one of the soldiers. The other soldier, Clement Nicholson, ran but was apprehended by the other officer and the servant as he tried to climb over a fence. The servant asked Nicholson how he had gotten to Charleston, to which Nicholson replied that a 'countryman' had gotten them drunk and taken them across the river in some kind of boat, and that once they realized where they were they did not know what to do. He was taken to the quarter guard of the 38th Regiment.
Put on trial for desertion four days later, Nicholson testified that as he was going to dinner at one o'clock on the 24th he met with a fellow soldier who invited him for a drink. On their way to it, they met a countryman who promised them some liquor if they would come with him. They did, and drank so much that they became insensate until they realized that they had been taken across the river. When they saw officers approaching, they feared being taken up as deserters. Figuring that they would fare better if they returned to camp than if they were taken by the officers, they tried to run.
Nicholson called upon two officers to testify to his character. The adjutant of the regiment considered him to be "a very sober diligent Man" who had never been punished or brought to a court martial before. Another officer had "always heard a good Character of the Prisoner before he was inlisted" and that he subsequently "always behaved like a good Soldier."
Nicholson was found guilty and sentenced to receive one thousand lashes given out in four sets of 250 each. We have no information about whether the sentence was administered in its entirety or partially remitted. We do know that Nicholson recovered fully from whatever punishment he received. He was in the regiment when it fought at Bunker Hill on 17 June 1775, and he was wounded in the battle. He died of those wounds two months to the day later, on 17 August 1775.