It also saw the talent of Cebuanos Jimwell Torion and Junthy Valenzuela along with other provincial cagers Rene Suba and Jun Carmona.

Red Bull was allowed to take six players from their PBL team and took Kerby Raymundo, Davonn Harp, Lordy Tugade, Jimwell Torion, Junthy Valenzuela and Bernard Tanpua.

Tutt returned for the 2000 Governors Cup, and the renamed as the Batang Red Bull Thunder made a strong showing to finish in third place at the end of the tournament, their first trophy in the league.

In 2001, Red Bull finished seventh in the All-Filipino Conference and met eventual champion San Miguel Beermen in the quarterfinals.

But in Game five, Red Bull won 79–77 after a potential game-tying basket by San Miguel import Nate Johnson was blocked from behind by Miller with no time left.

In the Governor's Cup, Tutt returned for the team in hopes of claiming back-to-back title, but the Thunder was eliminated in the quarterfinals.

The Thunder dominated the tournament, eliminating Shell in the quarterfinals and the Beermen in the semis to face the Talk 'N Text Phone Pals in the finals.

In 2003, The Thunder used their first round pick to select 2002 UAAP MVP Enrico Villanueva from Ateneo de Manila to bolster Red Bull's frontline.

But the deciding game was marred by a vicious clothesline of Torion on Phone Pals' point guard Jimmy Alapag.

Red Bull made its third Finals appearance in 2004, losing to eventual champion Barangay Ginebra in the transitional tournament dubbed as the 2004 Fiesta Conference.

During the 2004–05 Philippine Cup, Red Bull was decimated with the departures of alleged Fil-Shams (Filipino-Americans that did not prove their Filipino blood) Mick Pennisi and Davonn Harp, who were deported after the Department of Justice found them to have falsified their documents.

But the event paved the way for guys like Tugade, Valenzuela and Enrico Villanueva to shine as Red Bull recovered to place fourth in the 2005 Fiesta Cup.

During their title run, the Bulls replaced import Quemont Greer in place of a more team-oriented James Penny at the start of the quarterfinals.

Red Bull swept Alaska in the quarterfinals while surviving a seven-game tussle with crowd-favorite Barangay Ginebra Kings in the semi-finals.

In the middle of the elimination round, Red Bull traded 2005–2006 Fiesta Cup Finals MVP Lordy Tugade to the San Miguel Beermen alongside reserve Omanzie Rodriguez in exchange for future draft picks.

In the Philippine Cup, Red Bull placed third after the elimination round with an 11–7 win–loss card and an outright quarterfinals berth in which they defeated the Sta.

Red Bull gained the top seed in the Fiesta Conference but dealt Enrico Villanueva to San Miguel Beermen for Rommel Adducul.

Although the Barakos posted an identical 11–7 card in the 2008 Fiesta Conference, they managed to finish second to earn themselves a seventh-consecutive semifinals appearance.

With Mexico national basketball team mainstay Adam Parada as their import, Red Bull faced the rampaging Barangay Ginebra Kings with a 6-game winning streak in the semifinals.

Prior to the 2008–09 season, they lost Mick Pennisi who went to San Miguel Beermen and Topex Robinson who went to Purefoods TJ Giants and got rookies Larry Rodriguez, Jeff Chan, and Mark Cuevas.

But there are also some players who went to Red Bull and started a new beginning like Gabby Espinas from Air21 Express and Mike Holper from Barangay Ginebra Kings.

The newly christened Barako Bull Energy Boosters, with team manager Andy Jao, hired former PBA Rookie of the Year Leo Isaac as its new head coach with Ariel Vanguardia of the JRU Heavy Bombers and former Philippines women's national basketball team coach Raymond Celis as chief lieutenants.

In the first weeks of the Philippine Cup, they signed undrafted rookie Hans Thiele and eventually became the team's top scorer together with Salvacion.

On January 20, 2011, the management of the Energy Boosters announced that they will take a leave of absence for the upcoming Commissioner's Cup to make way for the Smart Gilas Philippine national team.

In a letter sent to PBA Commissioner Chito Salud, the owners of the Barako Bull franchise mentioned their ongoing legal battle against TC Pharmaceuticals Industries, Co. the manufacturer of Red Bull in Thailand, and the death of one of their owners, Tony Chua during the onslaught of Typhoon Ketsana in 2009 as the main reasons why they will leave the PBA.

[11] After Crisano went public with his accusations, team management did not renew his contract after the 2009–10 season ended and had difficulty in getting his back pay.

Commissioner Chito Salud gave guidelines to Barako Bull for them to pay their standing obligations with the team members in lump sum.

[15] One of the SMC teams, the San Miguel Beermen, was renamed to Petron Blaze Boosters before the start of the Governors Cup.