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Aside from giving totally overpowered items like 15 endocrine boosters, never breaking devices, sub of doors and so on the safest way to kill any enemy in direct submarine combat save for pirates is

Remember that such thing as GODMODE DISCHARGE COIL IS ACHIEVEABLE

Set it's range to 999 and damage to 999999 and maybe power consumption to 2. You can clear nests with it too.

Have fun one-shooting doomworm every time. Those shocks also travel 25 times further through walls.

Ah yeah, how do we kill pirates? Well you can risk going up close and electrocutting them OR traditionally use a nuke via railgun into important part of ship. Just in case place multiple discharge coils.

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about 2 years ago - /u/Regalis11 - Direct link

You can also just modify the game code to unlock every achievement when the game starts or use Steam Achievement Manager. :^)

There's obviously tons of ways to build completely overpowered submarines in the sub editor, but personally I don't see the need to prevent that. If that's how you enjoy playing the game, go ahead!