Complex sentence: The Doctor chose to save the one he was closest to personally-ensign Harry Kim, and as time passed, began to be overpowered by guilt by what he saw as a personal choice to let Ensign Jetal die so that his friend could live.
Split into simpler sentences: The Doctor chose to save the one he was closest to personally-ensign Harry Kim. As time passed, the Doctor began to be overpowered by guilt by what he saw as a personal choice to let Ensign Jetal die so that his friend could live.