In 2002, Biaggi rode the four-stroke for the first time as development on the new motorcycle remained strong throughout the season. He won in Brno, Czech Republic and Sepang, Malaysia to clinch runner-up in the championship behind rival Valentino Rossi. In 2003, Biaggi finished third in the MotoGP championship after rejoining Honda on the Camel Pramac Pons team. It was expected that Biaggi would be one of the main candidates for the title in 2004, but a crash in Estoril saw his season begin to fade. At the end of the 2004 MotoGP season Biaggi finished the championship in third place, behind Sete Gibernau and series winner, Rossi.
Biaggi started the 2005 MotoGP season as an official factory Honda rider, joining American racer Nicky Hayden on the Repsol Honda Team with technical director Erv Kanemoto. It was hoped that continued cooperation with Kanemoto and the full factory support from Honda would make Biaggi one of the main title contenders in 2005. However, Biaggi finished the season fifth in the championship with only 173 points (series winner Rossi finished with 367).
Biaggi lost his ride for the 2006 season, his position filled by 2005 250cc Grand Prix champion, Dani Pedrosa. He negotiated with Honda, Kawasaki, and Suzuki, however, was unable to land a contract even with the backing of major tobacco sponsor Camel. On January 10, 2006, Biaggi posted on his website that he would not take part in the 2006 MotoGP season.
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