UAAP Season 65 (2002–03) saw the Blue Batters improve on its standing by placing 5th with a 2–8 win-loss record, surpassing the previous year record of 1-9 (6th place). UAAP Season 66 (2003–04) was remarkable as Ateneo defeated La Salle for the first time in over 13 years, 9–8. In Season 67 (2004–05), they finished with a 3–7 record to place 4th overall. It would have been the Blue Batters' first Final Four appearance had UST not swept the elimination round and was declared champions of UAAP Season 67.