Recommendations:
1. Find Rareware to unlock the Free Perk Machines.
2. Buy a Riot Shield.

Notes:
1. Find the first Rareware and open the first room.
2. Destroy the first two cameras, find the first two fuses and the first document.
3. Open the next door and obtain the first key card (see key card location below).
4. Use the key card and find the third fuse. Use the first computer terminal to unlock the next door and partially activate Missile #1.
5. Open the next two doors, find the fourth fuse and destroy the third camera.
6. In the next room use the four fuses to unlock the next door.
7. Advance downstairs and find the second document, Rareware and computer terminal.
8. Use the second computer terminal to unlock the next door and partially activate Missile #2.
9. Open the next room, destroy the fourth camera, open the first valve and turn on the power.
10. Advance downstairs and open the last valve. Use the third computer terminal to open the next door and partially activate Missile #3.
11. Find the two C4 explosives and the helicopter tracking bug.
12. In the next two rooms pressurize the fuel system and destroy the fifth security camera.
13. Open the engine room and kill the Mangler. Destroy the last camera, plant the two C4 explosives, find the third document and Rareware.
14. Use the two computer terminals to fully activate Missiles #1 and #2 (these are ready to launch now or later).
15. Open the next two doors and kill Brutus. Find the last document and use the last computer terminal to fully activate Missile #3.
16. Use the last keycard to open the garage and plant the tracking bug on the Apache.
17. Kill the two Panzers and find the last Rareware.
18. Launch the three Missiles from the front of the ship. (*An EE can be found if you drop inside Missile #1 before the hatch closes. It can also be accessed after all missiles have been launched by using the computer for Missile #1.)
19. The computer used to launch Missile #1 can now activate the garage computers.
20. Go back to the garage and use the computer to activate Missiles #4-8.
21. Launch Missiles #4-8.
22. Purchase the Buyable Ending to escape the ship.

#1. Inside the vault next to the buyable riot shield.
#2. Dropped by Brutus after he is killed.

#1 & #2: In the first room.
#3. In the Juggernaut room.
#4. Across from the power switch.
#5. In the engine room.
#6. Behind the speed cola machine.

#1. On a table in the first room.
#2. On the rack next to the second computer terminal.
#3. Under the stairs in the engine room.
#4. On the barrel in the garage.

#1. At the front of the ship.
#2. Next to the servers in the Speed Cola Room.
#3. Next to the engine in the engine room.
#4. Above the garage.

Inside the cabinet before the room where you pressurize the fuel system

Inside the wall cabinet that is next to the C4 cabinet.