C&C_Boarding_Party addon - Renegade Coop mod for C&C: Renegade

Continue to the ship's engines and take it offline, note that you need a hotwire to complete this objective. Find the Green keycard! An officer will mostlikely drop it when you kill them.
Use the Green Key to access the Ship's Mate quarters and kill him softly to gain Level 2 security clearance. Proceed to the prisoners and wait for the cinematic to finish :)

Warning: When the cinematic ends the prisoners will be under attack in the Submarine Bay, protect them at all cost or your mission will fail. If one dies is fine but not all of them. At least one prisoner must make it to safety aboard the Submarine.

Once this objective is completed you can use your new security clearance to go through the cargo section and sabotage the Nod torpedo racks by pressing E on them. You will now obtain the Red keycard. Return to the starting position and take the stairs to the red door. Proceed with caution as there are many enemies here. Take them out and finally kill the Ship's Captain to obtain an Ion Cannon Beacon and Ion the Pedestal to win the game.