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If you have a missile launcher, then consider hitting enemy shields with the missile (missiles bypass all shields), then use your other weapons to hit other rooms once the enemy shields are down and are no longer absorbing your shots. If the weapons are not threatening, then focus on shields to end the battle quickly. If the enemy weapons are extremely threatening, then focus your fire onto their weapons to disable them quickly. This is something that comes with experience your threat prioritization improves a lot once you can identify the specific weapons on the enemy ships just by looking at them. Your choice of targeting depends mostly on how threatening the enemy ship actually is.
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(Exceptions for this rule would include the Zoltan and Stealth ships, in which case it's arguable that you should upgrade engines a few levels before worrying about shields.) This allows you to completely wall the majority of enemy ships at the beginning of the game unless they have missile launchers of their own, which in turn saves you money on repairs. Click to shrink.For most ships, acquiring the 2nd shield bubble is usually the most important early upgrade.
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