Not sure if I'm doing something wrong. But it feels like the enemies are always too powerful that the only thing I can do is avoid them. Also never figured out what those wire looking things in the boxes are for and how to use them.
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Sorry if it was unclear. When you defeat enemies, they drop "souls" which you spend to open those boxes (you can see how many souls you have in the top left). The boxes give you items that improve your character and make it easier to get around and/or fight enemies. The game was balanced around you getting at least a few items per stage rather than strictly focusing on the ship.