JRU (JRC then) captured the NCAA crown which up to this date is the last time José Rizal won a championship.

As contrasted with SSC-R's five consecutive championships in the 1990s, JRC continued to struggle and not until 1999 where the Heavy Bombers made it to the finals but lost to the defending champion Letran Knights.

JRU was bannered by Ariel Capus, season MVP Ernani Epondulan, Rodel Milla, Joel Finuliar and razzle dazzle pointguard Erwin Estebal while San Sebastian was led by Mark Macapagal, Christian Coronel and Jam Alfad.

Not until the 2007 NCAA season when San Sebastian's Final Four chances was denied by José Rizal via a 7-point winning margin in a come from behind victory.

2 seed; the Heavy Bombers won the game and relegated San Sebastian to the fourth-seed playoffs where they were eliminated.

San Sebastian won the game 61–52, completing a season series sweep against the Heavy Bombers (also in 2002 and 2003) and making it a second consecutive finals appearance for the Golden Stags and faces last years' Finals tormentor and losing finalist San Beda Red Lions.

In 2017 both San Sebastian & JRU met in the semifinals for the first time since 2010 with the top-seeded Lyceum swept the regular season.

the 3rd-seeded Heavy Bombers (who swept the Golden Stags in the regular season that will give them an advantage) faces the 4th-seeded Golden Stags (who survive a scare from a stubborn Letran team that pave the way for them to enter the semifinals) but in that San Sebastian-JRU game was different as the Golden Stags emerged victorious after San Sebastian blew the game wide open as they led by 26 points heading in the 4th quarter despite JRU putting San Sebastian into the penalty situation early in the 4th quarter and managing to cut the deficit by at least 15 points but the resilient Golden Stags still won the game over the Heavy Bombers 85–73, to advanced to another knockout match against defending champions San Beda Red Lions.