[3] The allegations surrounding Morgan's disappearance and presumed death sparked a public outcry and inspired Thurlow Weed and others to harness the discontent by founding the new Anti-Masonic Party in opposition to President Andrew Jackson's Democrats.

[8][9] Morgan told friends and acquaintances that he had served with distinction as a captain during the War of 1812, and his associates in upstate New York appear to have accepted this claim.

[19][20] Morgan then attempted unsuccessfully to help establish or visit lodges and chapters in Batavia, but he was denied participation by members who disapproved of his character and even questioned his claims to Masonic membership.

[22] Morgan finally announced that he was going to publish an exposé titled Illustrations of Masonry,[23] critical of the Freemasons and revealing their secret degree ceremonies in detail.

[26] Since Masons place their hands on a Bible and promise not to reveal the passwords and grips of the degrees, several members of the Batavia lodge published an advertisement denouncing Morgan for breaking his word by authoring the book.

[31] While the jailer was away, a group of men convinced his wife to release Morgan;[32] they walked to a waiting carriage, which arrived two days later at Fort Niagara.

[32] The generally accepted version of events is that Morgan was taken in a boat to the middle of the Niagara River and thrown overboard, where he presumably drowned, since he was never seen again in the community.

[33] In 1848, Henry L. Valance allegedly confessed on his deathbed to taking part in Morgan's murder, a purported event recounted in chapter two of Reverend C. G. Finney's anti-Masonic book The Character, Claims, and Practical Workings of Freemasonry (1869).

However, the wife of a missing Canadian named Timothy Monroe (or Munro) positively identified the clothing on the body as that which had been worn by her husband at the time he had disappeared.

[42] C. T. Congdon, in Reminiscences of a Journalist, cites a third-hand account "that Morgan was murdered by certain very zealous Freemasons," and notes that the resultant anti-Mason sentiment caused many elections to go to non-Masons for a number of years afterwards.

[44] Unverified rumors speculated that Morgan had assumed a new identity and settled in Albany, Canada, or the Cayman Islands, where he was supposed to have been hanged as a pirate.

[48] In 1832, the Anti-Masonic Party fielded William Wirt as its presidential candidate and Amos Ellmaker as his running mate, and they received Vermont's seven electoral votes.

[13] By 1837, some historians believe that Lucinda Pendleton Morgan Harris had become one of the plural wives of Joseph Smith, founder of the Latter Day Saint movement.

[13] In 1841, the Mormons announced their vicarious baptism of William Morgan after his death, as one of the first under their new rite to posthumously offer people entrance into the Church of Jesus Christ of Latter Day Saints.

Other items found included a ring with the inscribed initials "W. M." The box contained a crumpled paper; its few legible words seemed to suggest that the remains might have been Morgan's.

[4]The pharmacist John Uri Lloyd based part of the background story of his popular scientific allegorical novel Etidorhpa (1895) on the kidnapping of William Morgan and the start of the Anti-Masonry movement.