John Ali, a senior official in the Nation of Islam during the 1960s who was a key figure in the organization’s fractious split with Malcolm X, died on July 26 at his home in Philadelphia. He was 98. His son, Jon Ali, confirmed his passing and noted that his father had recently relocated from Chicago.

Ali, born John William Simmons Jr. in 1927 in Avery, Georgia, was widely recognized as Elijah Muhammad’s national secretary and the Nation’s second-in-command during a turbulent period marked by internal conflict and external scrutiny. A graduate of Bryant University with a degree in accounting, Ali managed the Nation’s extensive business interests, including its involvement in the career of boxer Muhammad Ali, a prominent Nation member at the time.

Initially close allies—Ali and Malcolm X were once roommates—their relationship deteriorated amid growing tensions within the Nation of Islam. Malcolm X’s public criticisms of Elijah Muhammad’s leadership and extramarital affairs contributed to a widening rift. Following Malcolm’s suspension from the Nation in late 1963, John Ali publicly confirmed the disciplinary action. After Malcolm left the organization in 1964, Ali compelled Malcolm’s brother, Philbert X, to denounce him in a speech scripted by Ali.

Ali’s tenure was also marked by allegations that have shadowed his legacy. In 1963, journalist Louis Lomax accused him of acting as an F.B.I. informant, a charge Ali consistently denied. Declassified documents later revealed that the F.B.I. had surveilled both the Nation and Malcolm X extensively and used covert operations to exacerbate divisions between them.

The most enduring controversy surrounding Ali involves the 1965 assassination of Malcolm X at the Audubon Ballroom in New York City. On February 21, Malcolm X was shot and killed by gunmen affiliated with the Nation of Islam. Three men—Mujahid Abdul Halim (then Talmadge X Hayer), Muhammad Abdul Aziz (Norman 3X Butler), and Khalil Islam (Thomas 15X Johnson)—were convicted in connection with the murder. Halim admitted involvement but maintained Aziz and Islam were innocent; Aziz and Islam were exonerated in 2021 after spending decades in prison.

Ali was reportedly in New York the night before the assassination and met with Halim, fueling speculation about his possible involvement. While no concrete evidence has directly linked Ali to orchestrating the killing, researchers and historians continue to assess his potential role as an intermediary. Historian Abdur-Rahman Muhammad, featured in the 2020 documentary "Who Killed Malcolm X?," suggested Ali might have transmitted orders within the organization, though definitive proof remains elusive.

Despite decades of investigation, including work by Pulitzer Prize-winning biographers Manning Marable and Les and Tamara Payne, the full circumstances of Malcolm X’s assassination and the identity of key conspirators remain unresolved. Many witnesses have died, and relevant F.B.I. files remain classified.

After stepping down as national secretary in 1970, Ali remained involved with the Nation of Islam and expanded his business ventures, notably becoming the business manager of Main Bout, which controlled much of Muhammad Ali’s promotional rights. He amassed considerable wealth as the boxer rose to international acclaim.

John Ali is survived by his two sons, Jon and Sultan Ali; three daughters, Marie, Clara, and others; six grandchildren; nine great-grandchildren; and a brother, Michael. His death closes a chapter on one of the most enigmatic figures in the history of the Nation of Islam and one entwined with one of the most consequential assassinations in modern American history.