Scientists hope they [ will be discovering - will have discovered ] alternatives for fossil fuels soon. I'm not sure of the answer but I think it is will be discovering as it expresses the near future.
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I'm not a teacher
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Out of the two, I'd choose 'will have discovered', treating 'soon' as some sort of point by which the action will be completed.
Actually, I'd make it even simpler and go for 'will discover'.