Illness and Death (The Happy Battle)

Magalona, then 43, was diagnosed on August 8, 2008, with acute myeloid leukemia at the Medical City Hospital, Pasig City. Appealing to the media and the public, Maglona said:

I don’t want a media circus, [...] I want privacy with my family. What I’d rather talk about is how we can solicit blood donations to replace the supply that I have consumed in the hospital.

—Francis Magalona, August, 2008

After his first treatment and discharge, he made his return on Eat Bulaga together with Ely Buendia, who had also been recently discharged. Not wanting to let the disease get the better of him, he remained active, chronicling his battle with the disease on his blogs and continuing to pursue his creative efforts in spite of his illness. His daughter Maxene noted that "He always did what he wanted to do. He never let anyone or anything stop him from doing what he loved to do. He still went to the Camera Club, he still took pictures, every time he was discharged from the hospital, he recorded songs with Ely Buendia. He taught us that life is short but it can be well lived. Don’t waste your time in the world."

His wife Pia later described her husband's battle with the disease, saying "Francis was a very passionate person. When he was angry, he was very expressive. He would get angry with his cancer. That was his way of coping with it. But he didn’t give up. I remembered that he told me, 'I'm going down fighting.'

On March 6, 2009, at 12:00 p.m., Magalona succumbed to multi organ failure secondary to septic shock, secondary to to pneumonia in the immunocompromised (immediate cause); acute respiratory failure secondary to acute respiratory distress syndrome (antecedent cause); underlying cause: acute myleogenous leukemia blast crisis. He had undergone several chemotherapy sessions since he was diagnosed the previous year, and had been expected to undergo a bone marrow transplantation (BMT) and peripheral blood stem cell transplantation (PBSCT).

The announcement was first made on the television variety show Eat Bulaga!, which he had co-hosted. News of his death sparked a surge of web traffic to several Philippine news sites, causing a momentary slowdown in the operation of those sites. Guests at his wake included former president Corazon Aquino, along with other politicians and artists who paid tribute to Magalona's contribution to Filipino music, and to the national pride - the dominant advocacy theme in FrancisM's music. Fans arrived in droves to pay their last respects, some of them making a point to wear shirts from Magalona's FMCC line. Numerous television programs, ranging from noontime variety shows to primetime newscasts and late night news documentaries, paid tribute to Magalona.

Magalona had been slated to appear as a special surprise guest at the Eraserheads' "the Final Set" reunion concert on March 7, 2009. Since he died the day before, the band instead dedicated the concert as tribute to Magalona. Buendia rapped the 22-bar portion in Superproxy which FrancisM had written, and the penultimate song of their last ever Eraserheads performance was the reprise of Kaleidoscope World.

Magalona's remains were cremated before daybreak on March 11, 2009. After final rites, his ashes were then brought to his final resting place in the Loyola Memorial Park in Marikina City, causing traffic to stall in the Marikina Riverbanks area near the park as fans joined the convoy. Military rites and a salute were offered to Magalona, and his wife Pia accepted a Philippine flag from the Philippine Army, in recognition of Magalona's patriotism and for being an army reservist with the rank of sergeant.