Obedience has been and will always be absolutely crucial to the efficient performance of military forces. Compliance with orders was maintained through strict discipline. In 1867, the principle form of corrective action in cases of insubordination was confinement.

Ten incarceration cells were located at the fort. They were used for sentences not exceeding 42 days. Any sentence of seven days or more required a regimental court martial. Most minor crimes resulted in shorter terms than this.

Detention was solitary or mixed. In the case of solitary confinement, prisoners could not leave their rooms except to receive fresh air and exercise. Mixed imprisonment meant hard labour, such as drill in marching order, breaking stones, shot drill (moving cannon balls from one spot to another), cleaning barracks and privies.

For sentences under a week, soldiers were given a single blanket; longer terms meant that after the first week, bedding was provided, but it was removed every third night for the remainder of the sentence.

Rations reflected the nature of the crimes and ranged from full rations to bread and water. Alcohol and tobacco in any form were prohibited.

Discipline was governed by a graduated series of punishments to fit the crime. Minor crimes were drunkenness, lateness, poor turnout and insubordination. These resulted in confinement to cells with extra duty or loss of pay, or loss of good conduct badges.

Serious offenders who required considerable terms of imprisonment were sent to the penitentiary in Kingston.

Officers were governed by the same set of values as troops, but did not receive the same punishment. They were never sent to the garrison cells. Instead fines, confinement to quarters, extra duties or, in extreme cases, dismissal were in effect.

One of the punishments that was also used until 1881, was flogging. In 1854, a maximum of 50 lashes in one punishment was established; previously the number was 200. If a man passed out, he was revived and the punishment continued. Lashes were laid on by the drummers who in turn were lashed by the drum major if they were not using enough force.

Soldiers guilty of desertion were branded with the letter "D" (until 1871). Originally the branding was done by the drum major using needles and gun powder. In 1840 marking instruments were used and it became more like a tattoo. Another brand used was "B.C.", which referred to Bad Character. Prior to 1867 these branded soldiers were usually sent to criminal colonies, such as Australia.

Executions were only implemented for crimes of mutiny, desertion, or violence against superiors, and were more common in wartime.

Note: Fort Henry was also used as a prisoner-of-war camp in both World Wars. In August 1943, nineteen German prisoners used the flushing tunnel of the privies to escape from the fort. Most were captured immediately. However, the last was not recaptured until September 1 in Clayton, New York.

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