This is a surprisingly weak article for a lefty publication. Its whole framing is neoliberal, and all it can manage to say about Prabowo's past is that he was "alleged" to have participated in the massacres in East Timor.

The Intercept was much more straightforward when it said:

Prabowo, as Suharto’s son-in-law, was a senior commander of the massacres in occupied East Timor. In one, at Kraras in 1983 on the mountain of Bibileo, “several hundred” civilians were murdered, according to a United Nations-backed inquiry. Prabowo also personally tortured captives; one told me of Prabowo breaking his teeth.

Prabowo described himself to me as “the Americans’ fair-haired boy.” He worked hand-in-glove with the U.S. as he carried out massacres, torture, and disappearances — so closely that his fellow officers, he said, sometimes mocked him as “the American.”