How do I get rid of the aliens near the Ship?
You will need to somehow repel them away from there.
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Have you done any cooking yet? Come back after you have.
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So you've made your very own homemade alien REPELLENT.
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You still need to find a way to use it.
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A glass from Gio's won't do the trick this time, they're too many.
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You will need to find a way to spray it.
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If you haven't already, go to the Curiosity Shoppe in the 50s and get the antique bug squirter from the box labeled "free."
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Now use the bug squirter on the pot with the finished repellent to fill it.
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Back at the present-day Harbor (when you're joined by your alien buddy), bravely face the dog that has come closer and use the bug squirter on him.
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It worked! He and his friends have all retreated to the lighthouse island.
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What's stopping them from coming back, though?
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You'll need to somehow cut off their connection to the main island.
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They're only connected to it by a narrow bridge, after all. A wooden bridge, too. In the 1600s, that is.
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And as the aliens are always there, you can stop them from crossing from whatever time is more convenient to you. They don't realize they can leave in the other times.
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Travel back to the 1600s and go up to the Ruins to see the lighthouse from above.
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There's a very precarious rock wall there, right at the edge.
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If you've had experience with knocking down walls, you'll know what to do.
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Do you have the blacksmith hammer?
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If not, pick it up from in front of the Stables.
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Use the hammer on the wonky wall to knock it down.
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Watch the resulting landslide destroy the wooden bridge that connects the lighthouse island with the main island. Those aliens are no longer an immediate problem.