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You want to maximize the number of beacons you visit each sector, and re-visiting areas is a waste of time & fuel. Times when you might not want to risk it is when your ship is low on fuel or health or the rebel fleet is close behind. Generally, if your ship is near the exit beacon and the rebel fleet is a substantial time away, you should always explore nearby areas to possibly gain scrap, missiles, drone parts, fuel, weapons and crew. Conversely, being ill-prepared may mean having to run away from enemies or taking heavy damage, which reduces scrap available for upgrades and makes you even less prepared for later sectors. Because the sectors get progressively harder, being well-prepared early means that you will defeat enemies more easily and take less damage, giving you more scrap and allowing you to be well-prepared for later sectors.
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