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In Chapter 14 Tom is stabbed twice by Silver. Jim sees this but is hiding in the bushes.
Allan has been killed by the pirates because he had refused to convert to the mutiny.
Tom hears Alan's screams (they echo) and realizes that Silver has had him killed. As Aslan has already said, Silver stabs Tom twice after this realization, but not before Silver has taken him down with a spear as he runs away;
"With a cry John seized the branch of a tree, whipped the crutch out of his armpit, and sent that uncouth missile hurtling through the air. It struck poor Tom, point foremost, and with stunning violence, right between the shoulders in the middle of his back. His hands flew up, he gave a sort of gasp, and fell.
Whether he were injured much or little, none could ever tell. Like enough, to judge from the sound, his back was broken on the spot. But he had no time given him to recover. Silver, agile as a monkey even without leg or crutch, was on the top of him next moment and had twice buried his knife up to the hilt in that defenceless body. From my place of ambush, I could hear him pant aloud as he struck the blows."
Treasure Island/ Chapter 14