Some were shot by vigilantes on motorbikes. Others had bullets in the head, execution style. In killing after killing, the police would only describe the victims as “drug suspects” who had resisted arrest, a charge that rarely stood up to even minor scrutiny. And yet the slaughter continued with impunity, at the behest of the man who was elected president of the Philippines, Rodrigo Duterte.

But on Tuesday, nearly three years after Mr. Duterte left office, a major step was taken toward accountability for thousands of Filipinos who have long sought justice for their loved ones. Acting on a warrant issued by the International Criminal Court, which had been investigating Mr. Duterte’s antidrug campaign, the Philippine authorities arrested Mr. Duterte at Manila’s main airport as he returned from a trip to Hong Kong. On Tuesday night, they placed him on a plane that was bound for The Hague, where the court is based, according to two people with knowledge of the matter.

The I.C.C. accused Mr. Duterte, 79, of crimes against humanity during his time as president and when he was the mayor of the city of Davao. His case will be a high-profile test of the court, which in recent months has sought the arrest of Israel’s prime minister, Benjamin Netanyahu, and the head of the military junta in Myanmar, Min Aung Hlaing, on the same charges as Mr. Duterte. But those orders are unlikely to come to fruition, much like the court’s warrant for President Vladimir V. Putin of Russia that was issued two years ago.