I highly recommend you to find and try to understand those secrets by yourself.

But if you're still eager to know then this might comfort you a bit:
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⠀⠀⠀⠀⠀! !! !!! FINAL WARNING /SPOILERS\ DO NOT CROSS !!! !! !
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• POWER EXPANSION MODE:
  This will boost your Engines and increase the provided power by a LOT.
  ***You'll need this one active for other hidden features to function***
  
  You need to USE and RECHARGE Main Battery at the same time while on Standard Power Mode, wait for a few seconds for it to activate.
  You'll need to prevent the RED Junction Box from breaking by repairing it almost continuously.
  There're a bunch of other minor conditionals but keep in mind that you need your sub in perfect conditions to use it, if not it'll be disabled. Having a full crew might help, so it's not recommended to use straightaway on a new Campaign.
  ⠀
• Place an "Alien Power Cell" in the "Alien Terminal".
  This will unlock the 3 next features
  ⠀
• ELECTRICAL DISCHARGE+++:
  This heavily modified EDC will fry any entity outside the submarine for the set duration.
  It has a very long range.This has a 60 cool down.
  
  On the Alien Terminal press the Red button to pass in "OFFENSE MODE".
  Fuel_Out value of the two Reactors combine must be above or equal "700".
  Then active POWER EXPANSION MODE and press on the Nav. Terminal the
  "{»¡¿¶}›∞≈™≈∞‹{¶¿¡«}" button.
  Then let the magic do the trick.
  ⠀
• PROTECTIVE FORCE FIELD:
  This will torn space around the submarine for the set duration inflicting "bleed".
  This has a 60 cool down.
  
  On the Alien Terminal press the Red button to pass in "DEFENSE MODE".
  Fuel_Out value of the two Reactors combine must be above or equal "700".
  Then active POWER EXPANSION MODE and press on the Nav. Terminal the
  "{»¡¿¶}›∞≈™≈∞‹{¶¿¡«}" button.
  Then let the magic do the trick.
  ⠀
• SENTIENT STATION MODE:
  It gives you 20 seconds to shoot with Alien Turrets ADDITIONALLY to Equipped Turrets while manning them.
  This has a 60 seconds cool down.
  
  On the Alien Terminal press the Red button to pass in "DEFENSE MODE".
  Fuel_Out value of the two Reactors combine must be above or equal "700".
  The submarine must not be moving.
  Then active POWER EXPANSION MODE and press the Alien button in Command room.
  Then man turrets.
  
  ⠀
• Coming soon: AI hijack/growth.

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⠀⠀⠀⠀⠀! !! !!! FINAL WARNING /SPOILERS\ DO NOT CROSS !!! !! !
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I won't explain more than that to you, you'll need to figure how to make use of them by yourself.
You lazy cheater. :p