Originally from Virginia, he arrived in Batavia in 1824, claiming to have served with distinction during the War of 1812. After some time in town, he joined the local lodge of Freemasons, but soon found himself quarreling with them. Upon quitting the lodge, he declared his intention to publish a book describing the activities of the Freemasons in detail, despite his oaths that he would never reveal the secrets he learned. At the same time, he also claimed that a local newspaper publisher David C. Miller, had given him a sizable advance for the work.
The local lodge responded by publishing an advertisement denouncing Morgan and attempting to attack his printing presses. When these efforts failed, a group of masons gathered at Morgan's house claiming that he owed them money. According to the law, he could be held in jail until the debt was paid. Hearing about this, Miller went to the jail to pay the debt. After several failed attempts, he finally secured Morgan's release.
A few hours later, Morgan was arrested again, this time for another apparent loan he had to pay back and for supposedly stealing a shirt. He was jailed again, this time in Canandaigua, but someone appeared, claiming to be a friend of Morgan's, and offered to pay his debt and have him released. Morgan was hesitant and tried to avoid getting into a carriage that was waiting for him outside the prison, but he was forced inside before a crowd of people, all of whom heard him calling for help.
The next day, the carriage arrived at Fort Niagara, a defunct fort on the U.S. border with Canada. He was held prisoner there for several days, except, apparently, for a boat ride to Canada, where a group of Canadian masons refused to take responsibility for him. Some time between 17 and 21 September, 1826, he disappeared.
There are several accounts of what happened to Morgan next. Most people believe that he was taken in a boat to the middle of the Niagara River and drowned. A body did wash up a few weeks later, but after several investigations, it was identified as the body of a Canadian man who had disappeared. On the other hand, the Freemasons deny to this day that Morgan was killed. Soon after he disappeared, Miller published his book, which became a best-seller, and some people have speculated that the disappearance was an elaborate publicity stunt. According to them, Morgan assumed a new identity and settled in Albany, Canada, or the Cayman Islands, or even that he was hanged as a pirate. New York governor De Witt Clinton, himself a Mason, offered a sizable reward of $2,000 for any information about Morgan's whereabouts, but no one ever claimed it. The three men who had kidnapped him were sentenced to terms of no more than one year, since kidnapping was only a misdemeanor at the time.
Morgan's disappearance--and the minimal punishment received by his kidnappers--sparked a series of protests against the Freemasons throughout New York and the neighboring states. Under the leadership of Thurlow Weed, an anti-masonic, anti-Andrew Jackson (Jackson was a Mason) movement became a political party and even ran for the presidency in 1828, gaining the support of such notable politicians as William H. Seward. Its influence was such that other Jackson rivals, including John Quincy Adams, denounced the Masons. In 1832, the party fielded William Wirt as it presidential candidate, though the party only received seven electoral votes. Three years later, the party had disbanded everywhere but Pennsylvania, as other issues, such as slavery, became the focus of national attention.