Rossi had joined Honda's factory Repsol team for the 2002 season, the first year of the new MotoGP formula, riding the RC211V. He won the 2002 and 2003 championships comfortably, giving Honda back-to-back titles in the new era. Despite this success, reports during the 2003 season pointed toward a breakdown in the relationship between Rossi and Honda management, with tensions arising over commercial arrangements and the degree of priority given to his development program relative to other factory riders.
Mid-season rumours in 2003 suggested a possible move to Ducati, but Rossi rejected the Italian manufacturer, partly due to competitiveness concerns and partly due to misgivings about their approach. Ultimately, Rossi signed with Yamaha reportedly for a fee in excess of US$12 million for a two-year contract — a sum no other manufacturer, including Honda, was willing to match. His final win for Honda came in the Valencian Community round at the close of 2003.
Rossi made the switch from Honda to Yamaha and began the 2004 season in South Africa, where he took pole position and won the race after a hard-fought battle with Max Biaggi. The victory made him the first rider in premier-class history to win consecutive races with different manufacturers, as he had won the final 2003 race for Honda and now opened 2004 for Yamaha.
A 23-race podium streak was interrupted by fourth-place finishes in Spain and France, but Rossi responded with three consecutive victories in Italy, Catalunya, and the Netherlands. He retired in Rio de Janeiro and finished fourth in Germany, then won the British round from pole. Further victories followed in Portugal, Malaysia, Australia, and the Valencian Community round. Rossi finished the season with 304 points to runner-up Sete Gibernau's 257, clinching his third MotoGP title, his fourth premier-class title, and his sixth world championship overall — in the penultimate race of the year.
The 2004 title with Yamaha demolished the widely held assumption that the RC211V, rather than Rossi's talent, was primarily responsible for Honda's recent dominance. Honda, now without Rossi, failed to win the riders' championship in 2004; the RC211V's satellite riders — Sete Gibernau, Alex Barros, and others — competed for race victories but could not match the consistency Rossi brought to the YZR-M1.
The move reshaped competitive dynamics in MotoGP for years. Yamaha, reinvigorated by Rossi's arrival, became a genuine rival to Honda across the mid-2000s. For Rossi, the Yamaha seasons of 2004 and 2005 — back-to-back titles — represented the peak of his competitive dominance in the MotoGP era, and the 2004 switch itself became a defining moment in his legacy as the sport's singular talent of the decade.