Johnson led the Cup Series in points for much of the 2004 season, and entered the first Chase for the Nextel Cup second behind Gordon. Johnson won four races during the Chase, but finished in second, just eight points behind Kurt Busch. Johnson again led the Cup Series in points for much of the 2005 season, but lost the points lead after a hard crash at the Brickyard 400, and finished the season fifth in points. Johnson scored his first Daytona 500 victory in 2006, despite crew chief Chad Knaus serving a four-race suspension for rules infractions. Johnson also won the All-Star Challenge, Brickyard 400, and his first Nextel Cup championship in 2006. Johnson won the championship again in 2007, winning 10 races, the most by a driver in a single season since Gordon won 13 in 1998. Hendrick Motorsports won 18 of 36 races in 2007, including four in a row during the Chase.
