During the summer, the Ateneo-Hapee team joined the commercial and amateur Philippine Basketball League and won the championship under coach Joel Banal. At the start of the 65th season of the UAAP, with a championship caliber coach in Banal, the Ateneo de Manila community had very high hopes of finally ending the 14-year drought. The Eagles ended with 4 wins and 3 losses in the first round of the tournament, but lost their next two games, giving them a record of 4 wins and 5 losses. Most of the Ateneo community had lost hope. The Eagles, however, pulled off 5 straight wins, to end the elimination round with 9 wins and 5 losses. Furthermore, they spoiled the De La Salle Green Archers chances of sweeping the 14 game eliminations, which would have given them an outright berth in the championship round. Larry scored 15 points and grabbed 6 rebounds in that 76–63 win over the Green Archers. The Eagles would then face the UE Red Warriors. The team won both games and faced the De La Salle Green Archers in the finals in a best of 3 series. In game 1, Larry scored 11 points including 3 three points, with 6 assists and 2 crucial blocks against Mark Cardona in the game's dying seconds. In game 2, Larry scored his career high of 25 points but lost the game by 7 points. In game 3, Larry scored only 6 points because of food poisoning, but the team finally ended the 14 title year drought winning the UAAP Men's Basketball Championship with the score of 77–70. Larry was named co-Finals MVP, along with Wesley Gonzales, averaging 11.7 points per game.
In 2003, the Blue Eagles made it to the Finals but lost to the FEU Tamaraws.
In 2004, Larry's last year, he only played 4 games in that season, getting an ACL injury on his left knee while driving to the basket in the fourth game against UP that ended his UAAP career.