After a struggle with CEO Michael Eisner, Roy Disney's influence began to wane as more executives friendly to Eisner were appointed to high posts. When the board of directors rejected Disney's request for an extension of his term as board member, he announced his resignation on November 30, 2003, citing "serious differences of opinion about the direction and style of management" in the company. He issued a letter criticizing Eisner for mismanaging the company, neglecting the studio's animation division, failures with ABC, timidity in the theme park business, instilling a corporate mentality in the executive structure, turning the Walt Disney Company into a "rapacious, soul-less" conglomerate, and for refusing to establish a clear succession plan.
After his resignation, Disney helped establish the website SaveDisney.com, intended to oust Michael Eisner and his supporters from their positions and revamp the Walt Disney Company. On March 3, 2004, at Disney's annual shareholders' meeting, a surprising and unprecedented 43% of Disney's shareholders, predominantly rallied by former board members Roy Disney and Stanley Gold, voted to oppose the re-election of Eisner to the corporate board of directors. This vigorous opposition, unusual in major public corporations, persuaded Disney's board to strip Eisner of his chairmanship and give that position to George J. Mitchell. The board did not give Eisner's detractors what they really wanted: his immediate removal as chief executive. Roy Disney's campaign regarded Mitchell himself unfavorably; 25% of shareholders opposed Mitchell's re-election to the board in the same election.
As criticism of Eisner intensified in the wake of the shareholder meeting, however, his position became increasingly tenuous, and on March 13, 2005, Eisner announced that he would step down as CEO on September 30, one year before his contract expired. On July 8, Roy and the Walt Disney Company, then run by Eisner's long-time lieutenant, Bob Iger, agreed to "put aside their differences."