San Diego's high hopes for Leaf were soon dashed, as his rookie season was marked by poor behavior. Before the season started, Leaf skipped the final day of a symposium that was mandatory for all players who were drafted, resulting in a $10,000 fine.[12][13] In a prank customarily played on rookies, a group of Chargers players went out to dinner during training camp and charged it to Leaf's credit card. Rather than enduring this typical rookie prank, Leaf complained to Chargers general manager Bobby Beathard and refused to pay the bill, annoying his teammates. Several days later, during a practice play in which Leaf threw an interception, teammate Junior Seau knocked Leaf down with a hard hit. Seau's teammates immediately saluted him with high-fives.[14]
Leaf did well in the preseason, and led the Chargers to win his first two regular season games as a rookie,[10] the first quarterback to do so since John Elway in the 1983 NFL season.[15] But in the third game of the season he completed one of 15 passes for four yards, threw two interceptions, and fumbled three times in a loss against the Kansas City Chiefs.[16]
Leaf was benched after throwing two touchdown passes and thirteen interceptions in nine games, and was replaced by quarterback Craig Whelihan.[17] In ten games that season, Leaf threw two touchdown passes and fifteen interceptions, passing for 1,289 yards and having a 45.3 percent completion rate, with a poor quarterback rating of 39.[18]
Leaf had a bad relationship with the media and his teammates, whom he tended to blame for his poor play.[8] In a locker room incident during Leaf's rookie year, he was caught on camera screaming "Knock it off!" at San Diego Union Tribune reporter Jay Posner, and was physically restrained by Seau. Another on-camera incident involved Leaf reacting to heckling from a fan during a practice session,[6] and two coaches had to restrain him and escort him off the field. Leaf developed a reputation for poor work ethic and he was occasionally found at the golf links while the other quarterbacks were studying film.[19] After Leaf's rookie season ended, Chargers safety Rodney Harrison described it as "a nightmare you can't even imagine. If I had to go through another year like that, I'd probably quit playing".[20]
Leaf missed his second season due to a shoulder injury uncovered by a pre-season physical.[15] He was placed on injured reserve but made headlines for getting into a shouting match with Chargers general manager Bobby Beathard and another coach. The incident resulted in a fine, a suspension without pay and an apology by Leaf four weeks later.[21][22]
During his suspension, Leaf was caught on video playing flag football at a San Diego park, an act the Chargers alleged was a contract violation.[23][24] Leaf allegedly lied about a hand injury in order to get out of practice so that he could play golf.[19]
In the final game of the 2000 preseason, Leaf completed a pass to Trevor Gaylor to seal a 24-20 win over the Arizona Cardinals. Afterwards, Leaf appeared on the cover of the September 4, 2000 issue of Sports Illustrated along with headline "Back from the Brink", and the cover story speculated that Leaf was having an "ascent from pariah to possible standout pro passer".[24] Leaf started the first two games of the 2000 season, completing less than half of his pass attempts and throwing for five interceptions and one touchdown. When backup Moses Moreno went down with a strained knee ligament, the Chargers gave Leaf more playing time. However, he injured his wrist while throwing an interception in a week four game and did not play again until week eleven.[15] Following more poor performances and injury problems, he was released by the Chargers after the season, with four wins as a starter in three years.[25]