File 1 - Chapter 8 Part 2
Go down the long passage after the shop, and climb the ladder behind the machine gun. Continue until you reach the end of the mission, succesfully protect WRO soldiers, unlock 40 locks, and the laser gate will be unlocked. Enter the passage, and follow it until the end. Climb the ladder, and get the G-File and a few items.
File 2 - Chapter 10
After completing the motor cart portion, you come to a broken road where you must defeat some DG soldiers with the protect status. Continue until you reach the rooftop, go around the corner under the staircase that you came from, and the G-file is in plain view.
File 3 - Chapter 11
In the room with 4 Mako Points, just before the airship boss. Here you can get the last G-file, it's located on the pipe above you. You need to stand on the plate in the center of the room, wait until it rises high enough, you can jump on the pipe. The G-file is in the North corner.
Now that you have all three, continue the game. Upon beating the last boss, there will be an extra scene after the credits. Congratulations!