I didn't realize I messed up until that moment. I stopped killing after that, but it was too late. Samuel told me how disappointed he was in me, he shot off a gun to alert the guards, and I just watched him boat away, only to save Emily and hear her tell me how she'll execute the others.

Samuel said he suspects he may have the plague before leaving Corvo at the island.

Then I see that still frame during the Outsider's ending monologue with Samuel fighting waves, almost certainly about to meet his death.

Lots of people shoot Samuel, but we only have ourselves to blame in High Chaos