John Allan was born January 3, 1746, in Edinburgh Castle, Scotland, where his parents sought refuge during the Jacobite Rebellion.  He was the son of William Allan, a British officer, and Isabella Maxwell, daughter of Scottish gentleman Sir Eustace Maxwell.  Once the country was at peace again and full of soldiers without work, many were sent to settle Nova Scotia.  Young John and his family, along with approximately 2,000 other colonists, arrived in Halifax in 1749.

After several moves, the family finally settled in on a large grant of land between New Brunswick and Nova Scotia.  At some point during his youth, it is believed he went to school in Massachusetts, and there became sympathetic to the American cause.  On October 10, 1767, at the age of 21, he married Mary Patton and together they lived on his farm of 648 acres called “Invermary.”  He held several prominent positions in Nova Scotia including Justice of the Peace, Sheriff, Clerk of the Sessions and the Supreme Court, and Representative in the Provincial Assembly at Halifax.

Allan was outspoken in his support of the American colonists, which made for dangerous times in Nova Scotia.  Convinced that his apprehension was imminent, Allan fled Nova Scotia on October 3, 1776, in an open boat, leaving his wife and five children behind.

After meeting with the men of Machias for a few days, Allan realized that defending the isolated and vulnerable easternmost border would require the assistance of the local Indians, so he set out to secure supplies from the Massachusetts Council.  Allan sailed from Machias sometime in late October of 1776, and from the Piscataqua River took a stage to Boston, where he arrived on the 7th of November.  Council was unable to promise any aid as supplies were already scarce at home, so Allan decided to visit Congress in Philadelphia to plead his case.

Along the way, Allan fell in with General Horatio Gates, whom he accompanied to the headquarters of General George Washington.  Allan was presented to Gen. Washington and dined with him on December 22nd.  On Christmas Day, Allan continued on his journey, and the next day received word that Gen. Washington had crossed the Delaware to attack Trenton.

Allan arrived in Baltimore, where Congress had moved in anticipation of a British attack, on December 30th.  He was received by Congress on January 4th and gave them a full report of the eastern frontier.  At his urging, Congress authorized Massachusetts to raise an expedition to seize Fort Cumberland and proceed to Halifax to destroy the Royal Navy’s dockyard.  Allan was also appointed Superintendent of the Eastern Indians and Colonel of Infantry, receiving his instructions from the Honorable John Hancock.

On his way back to Boston, Allan learned of a failed attack on Fort Cumberland by fellow Nova Scotian refugee, Jonathan Eddy.  In retaliation, British soldiers burned the homes of rebels, including Allan’s, forcing his family into hiding.  Once found at the home of his in-laws, his wife was arrested and transported to Halifax where she was held prisoner for 6-8 months.  When asked to reveal the whereabouts of her husband, she is said to have told her captors that he had “escaped to a free country.”

Col. Allan remained in Boston for three months where his plan, already approved by Congress, was scaled back by the Massachusetts Council to allow only a single regiment to occupy the St. John River valley.  Upon his return to Maine, he established friendly relations with the Indians along the ill-defined border of the St. John River, but the British arrived shortly thereafter in large numbers forcing Col. Allan to return to Machias in defeat.  Although some of the Indians were swayed by the promises and gifts of British counterpart Michael Francklin, a large number of loyal warriors and their families joined Col. Allan on the difficult journey through the inner lakes and rivers back to Machias.

Back in Machias, representatives arrived from other tribes including the Passamaquoddy, Micmac and Penobscot.  The timing couldn’t have been better as the British arrived in Machias on August 14 prepared to level the town.  As they headed up the river, Col. Allan and his men, including the Indians, lined up along the banks of the river and at some point they let up an Indian yell.  Hearing the sounds echoing through the hills, the British feared they were grossly outnumbered and retreated.  Machias was never seriously threatened again.

Food and supplies were always scarce, the worst time being the fall of 1780 when conditions were close to a famine.  As his requests for more supplies were ignored, Col. Allan felt it necessary to return to Boston for a personal interview with Council.  Fearing that he might never return, the Indians demanded security.  By this time Col. Allan had been reunited with his family in Maine, and so it was arranged that he would leave his two eldest sons, Mark and William, with the Passamaquoddy as insurance.  According to Kidder, the boys were favorites with the Indians; likewise, Mark and William had a lifelong attachment to them.

Col. Allan remained in Machias until he resigned his position at the close of the war.  He opened a general store on an island he named Dudley’s Island, later known as Allan’s Island, and now called Treat Island in Passamaquoddy Bay.  After two years he closed the store and retired to Lubec Mills, where he resided until his death on February 7, 1805.