The rivalry started in 1972 when José Rizal was playing in the championship against new member San Sebastian. The Heavy Bombers was bannered by Philip Cezar, David Cezar, Ed Carvajal, Jess Sta. Maria, Cris Calilan, Olimpio Santos, Jimmy Santos and Norberto Rivera. San Sebastian has their own superstar with the like of Dave Supnet. JRU (JRC then) captured the NCAA crown which up to this date is the last time José Rizal won a championship. Years later the two teams again figured in a mini rivalry, San Sebastian's Paul Alvarez and José Rizal's Vergel Meneses figured in a PABL Slam Dunk contest in 1987 in which Meneses won the contest. 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.
In 2000, the Golden Stags and the Heavy Bombers met in the Final Four. JRC clinched the No. 1 seed while SSC-R got the 4th seed. The Stags defeated the Bombers twice to advance to the Finals against CSB. Thus, the Stags became the second (Letran did the trick in 1999 also against the Stags) 4th seed to upset the 1st seed in the Final Four. SSC-R and JRU also met in the 2001 Finals. 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. JRU lost in the series, which included a 33-point blowout loss in the deciding Game 3. Coronel was named as the 2001 NCAA Finals MVP.
The rivalry continued during Final Four appearances of both schools from 2002 and 2003. 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. The Stags was ahead by 7 points against the Heavy Bombers 1:10 to go in regulation. José Rizal capitalized on the errors of San Sebastian and force an overtime to win the game. This allowed JRU to grab the number 3 spot in the Final Four. JRU had another part in eliminating SSC-R in the 2008 season when they were tied for the number 2 seed with two other teams; in the ensuing classification playoffs JRU and San Sebastian met in the first round to decide which team will figure in a playoff for the No. 2 seed; the Heavy Bombers won the game and relegated San Sebastian to the fourth-seed playoffs where they were eliminated. In 2009 San Sebastian and JRU renewed their rivalry once again in the Final Four wherein a Jimbo Aquino-less-Golden Stags (whose serving a one game-suspension after committing a flagrant foul against San Beda for the 1st-seed playoff which also barred him from getting any individual awards) were beaten by the Heavy Bombers 72–65 in Game 1, But in Game 2 of their semifinals series with Jimbo Aquino returning from his suspension The Stags defeated The Heavy Bombers 79–64 and the Stags entered the Finals for the first time since 2003 wherein the Stags loses against the Letran Knights in 3 games. Eventually the Stags won the championship against the four-peat seeking Red Lions wherein the Stags had its vengeance on the Red Lions via sweep The Stags' Jimbo Aquino was named the 2009 NCAA Finals MVP and ending San Beda's dynasty San Sebastian won its last title since 2002 when they swept the St. Benilde Blazers. In 2010 San Sebastian and JRU once again met in the playoffs for the third consecutive year and second in the semifinals with San Beda's sweep of the elimination round which led to a stepladder format in the semifinals JRU and Mapúa figure it out in the first round in which JRU won 60–54 The Heavy Bombers advance to the next round against the defending champions San Sebastian Stags. But in that Part III of San Sebastian-JRU. 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.
The final four was instituted in 1997;[2][3] prior to that the first and second round winners, plus the team with the best overall standing if it did not win either round, participated in the championship round to determine the champion.
^San Sebastian swept the first round and JRC only won against PCU in the second round.
^San Sebastian swept the first round and JRC only won against PCU in the second round.
^Semifinals Game 1. JRU had a twice-to-beat advantage prior to the game. San Sebastian forced a rubber match. Trailing 22-38 at the half of Game 1, the Heavy Bombers greeted the second half with a fierce 18-0 run to lead by two, with 11:37 to go, but the Stags' Nurjamjam Alfad and Christian Coronel conspired to defeat the Heavy Bombers and secured the win. Alfad finished with 14 points while Coronel sank the important free throws to win the game.
^The Stags dominated the Heavy Bombers all throughout Game 2. Mark Macapagal pumped in 25 points, Christian Coronel had 19, and Nicole Uy contributed 15, including a one-handed slam that punctuated the Stags' dominance of the Heavy Bombers. San Sebastian lost to Benilde in the finals.
^Finals Game 1. The two teams clashed neck-to-neck all throughout Game 1 but the Stags are the better team in crunch time. The Heavy Bombers entered the final quarter with the lead when the Stags applied its pressure defense. Stags' Roy Falcasantos converted a layup in the last 48 seconds of the game to break a 74-all tieup then later converted a charity to give his team the win.
^Finals Game 2. JRU relied on the offense of season MVP Nani Epondulan, Joel Finuliar, Rendel Dela Rea, and Ariel Capus to register a 68–54 lead in the final quarter of Game 2 to keep the Stags at bay and then finally made a comeback to the series.
^Finals Game 3. Showing experience, the Stags never faltered from the start of Game 3, as they outclassed the Heavy Bombers by 33 points en route to their 10th NCAA championship. Nani Epondulan, the season MVP, tallied 13 points in the first half, but was made scoreless in the second half.
^Semifinals. It was a nip-and-tuck affair all game until JRU's Edward Attunga converted two free throws to give his team its first lead of the game, 85–84, with 59 seconds left. San Sebastian's Redentor Vicente was fouled on a drive, but split his charities to tie the game at 85-all with 22 seconds remaining in the final period. JRU's Wynsjohn Te had a chance to win the game but missed a difficult lay-up, sending the game into overtime. Defending champs San Sebastian's trifecta of Redentor Vicente, Clark Moore, and Michael Gonzales needed an extra five minutes to beat the Heavy Bombers and advance to the Finals. San Sebastian won against Benilde in the finals.
^Semifinals. The Stags used an explosive run in the third quarter to put the Heavy Bombers for good. San Sebastian's Redentor Vicente led the Stags with 19 points, including eight straight in a 10-0 run in the third quarter and gave San Sebastian its biggest lead, 62-53. San Sebastian lost to Letran in the finals.
^Stepladder semifinals. This is the first playoff appearance for JRU since 2015, and the first for San Sebastian since 2013. San Sebastian lost to San Beda in stepladder semifinals round 2.
^San Sebastian originally won 86–76.The NCAA forfeited the game in favor of JRU after San Sebastian player RK Ilagan was ruled ineligible to play for playing in a ligang labas game.
^San Sebastian lost to Letran in the First round stepladder semifinals.
Legend* Number denotes playoff seeding. Shade denotes final position. Finished as the champion Finished as the 1st runner-up Finished as semifinalist Lost in 4th-seed playoff Twice to beat advantage C Tournament cancelled
Notes
^2021-22 season was played in early 2022 and the tournament was held in into a round robin tournament instead of the usual double round eliminations.
^2023-24 season was played in early 2024 and the tournament was held in into a round robin tournament instead of the usual double round eliminations.
^Navarro, June (October 6, 2000). "Benilde vs SSC for NCAA plum". Philippine Daily Inquirer. Archived from the original on October 17, 2000. Retrieved April 1, 2021.