It was during this period when he removed his support for Mayor Rey Malonzo in 2000 due to accusations from city council members that Malapitan is "[ignorant] of parliamentary procedures".

[1] Malapitan ran for and won the mayoral position in 2013, promising to improve Caloocan's health care and education in a similar manner to Jejomar Binay's mayorship in Makati.

[13][14][15][16] However, the Peace Research Institute Frankfurt (PRIF) noted in 2020 that Malapitan's mayorship was characterized with a passivity towards President Rodrigo Duterte's war on drugs during its first year (2016–2017), with Malapitan asking the local branch of the Philippine National Police (PNP) to take charge of crime control and work vigorously against illegal drugs,[17][18] which PRIF claimed to have "resulted in a huge spike of deadly police violence" and "excessive levels of vigilantism" during this period.

[24] Sometime in 2017, Bishop Pablo Virgilio David of the Diocese of Kalookan met with Malapitan, Modequillo and lawyer Sikini Labastilla, all three of whom are members of the Caloocan City Anti-Drug Abuse Council (CADAC), to discuss how to better facilitate rehabilitation and drug prevention in the city during the drug war, which lead to the establishment of the Caloocan Anti-Drug Abuse Office (CADAO) the following year.

[32] On April 22, 2016, during the campaign period for the local elections, Malapitan was charged of graft and plunder with the Office of the Ombudsman over allegedly overpriced birthday gift packages for senior citizens of Caloocan.

Their sons Dale Gonzalo (Along) and Vincent Ryan (Enteng) are also in politics, currently serving as mayor and 1st district councilor of Caloocan, respectively.