Since the death of founder William Pierce in July 2002, the National Alliance has become increasingly unstable. Initially, it appeared that most members of the group had accepted Pierce's successor, Erich Gliebe. However, during his tenure, there have been a number of incidents that have caused dissension within the group. Shortly after assuming leadership, Gliebe ousted former deputy membership coordinator and rival Billy Roper from the National Alliance. Although some members were reportedly unhappy with Roper's efforts to promote unity with other white supremacist groups, the general membership appeared to like him. Just weeks before his ouster, Roper had organized one of the largest and most successful white supremacist rallies in recent years. After leaving the National Alliance, Roper formed his own white supremacist organization, White Revolution. Based in Arkansas, the group has received endorsements from most major white supremacist and neo-Nazi groups in the country and has attracted former members of the National Alliance. Meanwhile, Gliebe attempted to solidify his leadership position by visiting various regional National Alliance leaders, presumably to ensure their loyalty to himself.

Gliebe, however, caused another stir after the Southern Poverty Law Center reported in its Intelligence Report that he made disparaging remarks about other white supremacist groups at a National Alliance leadership conference. The remarks attributed to him stung some members of those groups, though they have not seemed to have created any significant animus towards the National Alliance on the part of other racist organizations

A more serious incident surfaced in late January 2003, when Maryland anti-Semite, Bill White alleged on his Web site that the federal government was investigating Gliebe on charges of tax evasion and embezzlement. White claimed that Gliebe received more than $30,000 in cash from "Eastern European distributors." White, who is not formally associated with the National Alliance, but who has ties to a number of members and former members (including Billy Roper), sent shockwaves through the white supremacist community with this announcement, although there is no evidence to suggest that it is true. Another sign of trouble within the National Alliance was the ouster by Gliebe of another prominent member of the group, Lawrence Myers, a journalist and photographer, whom Gliebe claimed was an informant.

Although Gliebe takes charge behind the scenes, he stays out of the public view and allows other leaders within the National Alliance to take a more visible role. David Pringle, the membership coordinator of the group and the head of its Alaska unit, is the most visible spokesperson for the group and often appears in the media. Pringle and Shaun Walker, the group's Western States Coordinator, have also started a radio show on the Hal Turner Network, a shortwave radio network that caters to white supremacists and anti-Semites. Kevin Alfred Strom, the editor of the National Alliance's National Vanguard Magazine, has taken over Pierce's role as the host of the group's American Dissident Voices radio broadcasts, and has also created a new news-oriented Web site that claims to involve the combined efforts of various "nationalists of different races, countries and cultures."

In addition to these activities, National Alliance members have continued recruitment and leafleting campaigns, as well as rallies and other publicity-gaining stunts. In different parts of the country, National Alliance members have "crashed" pro-diversity meetings to present their "pro-white" views and have also attempted to join in anti-globalization and anti-war demonstrations. Members openly participated in rallies against the war in Iraq, where they carried signs that railed against Israel and the Jews. The group has attempted to exploit the anti-war and anti-globalization sentiment of young white activists with the idea of recruiting them but their attempts have not been successful, since many people in these movements are aware of the group's neo-Nazi ideology.

National Alliance members have also continued to get in trouble with the law, and have been arrested on various charges, including murder. In October 2002, authorities arrested two members of the group, Sammy Compton and Christopher Weston Whitley, for beating a man to death outside a pool hall in Phoenix, Arizona. In March 2003, law enforcement officers arrested Chester Doles, the former head of the Georgia unit, in Lumpkin County on five felony charges, including firearms possession.