Assassination quests will require you to sneak into a specific location and kill an enemy commander without being noticed. You will fail the quest if you are seen by an enemy, so it’s imperative that you scout the designated area first with your camera before going after the commander. After killing him and looting his body, you get a bonus for hiding the body in one of the specified locations, then you will have to escape the area to finish the mission.

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Commanders will have a yellow tag, different than the red one other enemies have (left). Also, you can hide their bodies at designated spots for a bonus (right).

There’s a total of seven Assassination quests in the game, with the only rewards being for finishing three and all seven, in which you will receive a Rupees bonus.