How do you deal with the bee hives? There's one at the watchtower (which wasn't in video clips), and the goddamn bees cost me so much of my health! I thought throwing rocks at it would stop it, but nope! Even with the hive on the ground, the bees are still there! There was a note talking about needing something to deal with bees, but if it's something I need to find, I can't find it since I'm trying to play the game in the order that it wants me to, and I haven't ran into any tool or item before I have to go up the watchtower.
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You are on a right track. You can throw a rock so it will fall and if the hive is still too close to you throw another one on it so it will get further from your place. There is also another way but it includes secret weapon which you can obtain later so it is more of an easter-egg solution. I have to check if I included also third option but I believe the rock is the safest solution, just think about where will it fall