He later played for AGFA in the Philippine Basketball League but had a difficult time leading the Photokina franchise to the title, losing to Tanduay in championship matches.
He was regarded as the second-best big man of his class behind Rommel Adducul, and was highly sought after by then-SMB coach Ron Jacobs after seeing the potential in his rail-thin frame.
Ildefonso was also involved in some controversy after signing with the now-defunct Pangasinan Presidents of the MBA, having a live contract with AGFA and at the same time being selected in the draft.
The San Miguel Corporation franchise wanted the promising youngster in their ranks to be the future cornerstone of the team and this forced them to buy out his MBA contract.
In 2002, Ildefonso temporary left San Miguel to join the Philippine National Training Pool in the preparation for the 2002 Asian Games in Busan.
However, the former two-time MVP did not play in the All Star Game, as PBA commissioner Sonny Barrios accepted his request to be with his six-year-old daughter who was scheduled for chemotherapy treatment on the same day.
Despite having injuries to four key players, Petron Blaze Boosters defeated the heavily favored Talk and Text for the Governor's Cup Championship, slamming the Texter's bid for a grandslam.
On January 11, 2012, in a game against the Talk 'N Text Tropang Texters, Ildefonso scored a season high 22 points after going 11 of 14 from the field, including a baseline spinner that gave them an 81–80 lead entering the final two minutes.
In his final season, he played an important role by mentoring Petron's 2012 top draft pick June Mar Fajardo, to improve the latter's performances and rebounding.
When the 38th season ended, for the first time since he was acquired by San Miguel Corp.'s flagship franchise from Shell in a draft-day trade in 1998, Danny Ildefonso's name was conspicuously missing from the team's official roster.
[4] After being a free agent for the first time in his career and missing the early games of the 2013–2014 season, Ildefonso was signed by the Meralco Bolts to a one-conference contract.
[5] When asked upon the two-time MVP's arrival, head coach Ryan Gregorio said: “I honestly believe that DI still has what it takes to compete at a high level in the PBA.
[5] Ildefonso made his debut for Meralco on January 4, 2014, playing 29 minutes and scoring 14 points to help his team win 92–88 in overtime and stopping a 4-game losing streak.
[7] On March 2, 2023, while being an assistant coach for the Converge FiberXers, Ildefonso was activated as their 15th local player in the lineup, thus confirming his official comeback in the PBA.
[9] In August 2024, Ildefonso was cited and fined P20,000 by PBA Commissioner Willie Marcial for his Facebook feeder team statements on Dave's NorthPort Batang Pier pending agreement.
[11] As of the end of 2022–23 season[12][13] Ildefonso's life story, from his struggles with poverty in his younger years to his rise to basketball superstardom, were dramatized on Maalaala Mo Kaya in 2004, where he was portrayed by Victor Neri.