To begin the 2000 season, Henson sustained an injury in practice that required redshirt-freshman Navarre to start under center against Michigan's first opponent, Bowling Green.
Navarre's play in the opener earned him Big Ten Conference Offensive Player of the Week.
[4] Shortly after Michigan's win against Auburn in the 2001 Citrus Bowl, Henson announced he would come back for his senior season and forgo entering the 2001 NFL draft.
[7] On October 4, 2003, at Kinnick Stadium, Navarre established the school single-game record for most passing yards: 389 vs. Iowa.
[8] In his senior campaign, Navarre again led Michigan to a 10–3 overall record, and the team's first Rose Bowl appearance since the 1997 season.
During the regular season, Navarre amassed 3,331 passing yards and 24 touchdowns, posting wins over Michigan rivals, Notre Dame, 38–0; and Ohio State, 35–21.
In the 14–28 loss, Navarre had played his last game as a quarterback at Michigan; gaining 271 passing yards and one touchdown on 27 completions in 46 attempts.
He also held the records for most total offensive yards gained in a game (368 vs. Iowa in 2003) and in a season (3,240 in 2003) before being surpassed by Denard Robinson in 2010.
In 2003, Navarre led the Wolverines to their largest comeback in school history, overcoming a 21-point deficit as they defeated Minnesota, 38–35.