Ankle surgery forced Crouch to redshirt for the 1997 co-national championship-winning season. In 1998, Bobby Newcombe began the season as the starting quarterback, but he was sidelined by a knee injury after the first game and Crouch took over the starting duties. Against UAB, Crouch rushed for two touchdowns and completed 11 of 17 passes in his first career start. 1998 proved to be a chaotic season for the Cornhuskers. Crouch made another start before being replaced by a healthy Bobby Newcombe. Newcombe started the next five games, but was pulled in the middle of a game because of a PCL strain. Senior walk-on, Monte Christo, took over for Newcombe, and started the following week against Texas. With Texas leading 10-0 in the middle of the second quarter, Christo was pulled and replaced by Crouch. Crouch remained the starter for the rest of the season, which ended with a 23-20 loss to Arizona in the Holiday Bowl.
The next fall Newcombe was named the starting quarterback, and it was rumored that Crouch might leave the team. Crouch, however, was given significant playing time in the first and second games. He started the third game against Southern Mississippi, and Newcombe moved to wingback. Crouch led Nebraska in a season that saw NU avenge its only loss of the season in a rematch against Texas in the Big 12 Championship Game. The Cornhuskers finished the season with a 12-1 record and ranked No. 3 after defeating Tennessee in the Orange Bowl.
Crouch started every game in the 2000 season, which ended with a 66-17 trouncing of Northwestern in the Alamo Bowl. Nebraska's only losses during the 10-2 season were to eventual national champion, Oklahoma Sooners, and the Kansas State Wildcats.
In 2001 Crouch had his best year, breaking school or NCAA records almost weekly and appearing to be a serious contender for the Heisman Trophy. In the first game of the 2001 season, a 21-7 defeat of TCU, Crouch surpassed Tommie Frazier as Nebraska's all-time total offense leader. He became the Big 12 all-time career rushing quarterback in the emotionally charged game against Rice. The next week, against Missouri, Crouch was backed up near the goal line when he scrambled to escape from defenders and pulled off a 95-yard touchdown run, the longest in school history. Against Iowa State the following week, Crouch broke the record for career touchdowns by a quarterback. Crouch became only the fourth player in Division 1 history to both pass and rush for 3000 yards in a career with his performance against Texas Tech. Next, in a hard-fought game against defending national champion Oklahoma, Crouch again showed off his speed and playmaking abilities, this time serving as quarterback and receiver in a single play, the famous "Black 41 Flash Reverse Pass" in which Crouch made a 63-yard touchdown reception. By mid-November Crouch had set a school record for most career wins as a starter and became only the ninth quarterback in D-1A history to have won 35 games as a starter. The Cornhuskers were 11-0 going into the annual contest with Colorado the day after Thanksgiving. Crouch had a career day, setting the school record for offense yards in a single game with 360 yards. The Nebraska defense was dominated by the Buffaloes, however, and gave up a then-record 62 points to Colorado. The 62-36 loss appeared to have ended Nebraska's hopes of playing for the national championship and to have hurt Crouch's chances of winning the Heisman. Two weeks later, despite only throwing a paltry 7 touchdowns to 10 interceptions—a laughable ratio for any starter, let alone an award winner—Crouch was announced as the recipient of the award, edging out Florida's Rex Grossman and Miami's Ken Dorsey in the closest Heisman ballot since 1985. His outstanding season also was recognized when he won the Davey O'Brien Award for being the best collegiate quarterback in the nation during the 2001 season. In the meantime several highly ranked teams were upset and in the final BCS rankings, Nebraska beat out one-loss Oregon and two-loss Colorado to earn the No. 2 spot in the BCS rankings. The final BCS rankings were steeped in controversy since Nebraska had the chance to play in the Rose Bowl for the national championship despite not winning a conference or division championship. In the Rose Bowl on January 3, 2002, Crouch rushed for 114 yards against the Miami Hurricanes but was denied a touchdown for the first time since September, 1999. The No. 1 Hurricanes defeated the Cornhuskers 37-14, leaving Crouch with a 35-7 record as a starting quarterback.
Crouch was initially drafted by the St. Louis Rams of the NFL as a wide receiver, but still wanted to play quarterback. Crouch, however, was seen by NFL teams as being too short to play quarterback. His athleticism was seen as better suited for playing wideout, but a hard tackle by a defensive player caused him to have 150cc of blood drained from his leg. Because of the injury, Crouch left the team before playing a game.
In 2007 Crouch was expected to battle Michael Bishop, Damon Allen, Mike McMahon and Tom Arth for the Argos' starting quarterback position, but he eventually faltered because of injury. He began the season on the nine-week disabled list. After coming off the disabled list, Crouch was released by the Argonauts on September 6, 2007.
On April 9, 2011, Crouch attended a public workout for the United Football League's Omaha Nighthawks. On June 8, 2011, Crouch accepted an invitation to attend the Nighthawks mini-camp. On June 10, 2011, he was added to the Nighthawks official roster. The UFL has been on indefinite hiatus since October 20, 2012.
Crouch was a sales territory manager for a major medical device manufacturer in the US. Currently, Crouch is a vendor of playground and recreation equipment at Crouch Recreation in Omaha, Nebraska.