That season, he amassed 4,704 total yards—passing and rushing—and accounted for 47 touchdowns, earning recognition as the Associated Press Class 4A Player of the Year and a high school All-American.
Stewart had a nice start to the 1996 season with a big game against BYU in the Pigskin Classic, completing 20 of 28 passes for 232 yards, two touchdowns and no interceptions.
When McCown faltered, Stewart came off the bench to complete 12 of 17 second-half passes, only to see the Aggies lose on a 47-yard field goal with 19 seconds to play.
Stewart's chance came once again when McCown injured his left shoulder on a touchdown dive in the last game of the regular season, a 26–24 loss to rival Texas.
Despite suffering a hyperextended knee in the first quarter, Stewart bounced back to throw for 324 yards and three touchdown passes, including the fabled slant to Sirr Parker that sealed the 36-33 double-overtime victory, earning the Aggies an invitation to the Sugar Bowl in which they lost 24–14 to Ohio State.
Despite his ups and downs, Stewart finished his Texas A&M career with a 23–11 record as a starter, and led the Aggies to their only Big 12 Championship and first BCS Bowl appearance.