Francis M. Albums and Other Artist

The release of his third album, Meron akong ano! (I Got Some!) in 1993 marked the beginning of Magalona's experimentation with Pinoy rock. It also saw the birth of Hardware Syndrome--previously known as Cannabis--the band which would, with Magalona at its helm, introduce the merging of Pinoy Rock and Rap to the Filipino music audience. Members over the years included musicians Carlo Sison,Francis Villanueva, Niño Mesina, Boyet Aquino, Elmer Blancaflor, Noel Mendez, Perf de Castro, Benjie "Bagets" Mendez, Albert Tamayo, DJ Kimozave, DJ Radikal MK, Kenji Marquez, Jack Rufo, and Wendell Garcia.

Magalona was soon cited for excellence in both genres of music. He frequently collaborated with other OPM luminaries such as Joey Ayala, Heber Bartolome of Banyuhay, Ryan Cayabyab, Mike Hanopol of Juan Dela Cruz Band, Andrew E., Michael V. and the Eraserheads. In the latter part of his career, Magalona worked together with Gloc 9 and Parokya ni Edgar. In 1994, Magalona moved from Octo-Arts EMI Philippines, which had released all of his previous albums, to BMG Records Pilipinas, the same label as the seminal Pinoy rock group, The Eraserheads.

Freeman was released the following year, 1995, and firmly established Magalona's legitimacy in the Pinoy rock scene. Tracks like "Three Stars & A Sun", "Kabataan Para Sa Kinabukasan", "Suckin' on Helium/Kaleidoscope World" would become defining touch-points in Magalona's body of work. A track titled "Intellectual Property Rights" would sample a speech by then-president Fidel V. Ramos. Intellectual property rights was an issue that would continue to be an important and very personal advocacy for Magalona. "Kaleidoscope World" went on to win 1996 Awit Award for Best Produced Record of the Year, and the 1996 NU 107 Rock Award for Song of the Year. Its music video was directed by the celebrated director/cinematographer Raymond Red

Magalona's next album,Happy Battle, was released in 1996. The launch for the video-game themed album at the Hard Rock Cafe in Makati was noted by the press for its wide range of influences: aside from fans of Magalona's music, he had showbiz fans and coworkers from Eat Bulaga!, where he had already started hosting; and two sets of Sony Playstations with giant screens set up so people could play video games while watching the gig. The album was also notable for a number of significant collaborations: "Unstrung Heroes" with Ely Buendia; "Sapot", with project band Planet Garapata, which included Raimund Marasigan, Jeng Tan and Mark Lakay, who would later form Sandwich; and "Make Your Move" with pioneer Filipino punk band Betrayed. In keeping with the nationalistic theme in Magalona's work, 1-800-Ninety-Six was written in celebration of the centennial of the Philippine revolution of 1896. "Rainy" won Best Folk song, and the album itself would became the first and only album to win Best Rock and Best Rap Album at the Katha Awards. When Magalona was diagnosed with Leukemia, he and his wife Pia would use the album name "Happy Battle" as a reference to his fight against cancer.