What does Ralph mean when he says only two and they've gone in lord of the flies?

Answer 1

he was referring to the casualties that took place. 'Only two' have died.

Answer 2

When Ralph says "only two and they've gone" in Lord of the Flies, he is referring to how only himself and Piggy remain as the rational, civilized individuals among the group of boys on the island. The rest of the boys have descended into savagery and chaos, symbolizing the loss of innocence and societal values.