During Part D of "Prologue: First Contact", after you are finished training, you must return to the instructor in the control room where the door will close behind you before being attacked by four Marines. However, if you walk through the door and then use Timeshift to run back through the door before it closes (or cheat using console commands to freeze time to perform the trick), you can then enter the door that the four Marines rush out of and access a secret area, although you need to reload from a previous checkpoint to get back into the game proper.

The second room at the left end of the hallway houses four tables with scaled down versions of several in-game models in various situations:
• The first table shows a large group of smaller Marines sitting on rugs in front of a larger Marine.
• The second table shows two models of a girl character fighting a T-posing Marine.
• The third table shows three small Marines and a crate, with two of the Marines on the floor waving up to the third who is dangling from the edge of the table.
• The fourth table shows a Marine trapped in a glass container with three guns aimed at him as he stumbles back-and-forth panicking.

There are Warp Pipes that can be found within the game's first and fourth chapters that strikingly resemble the Warp Pipes from the Mario series. Upon entering either Pipe, there will be a secret room with three more Warp Pipes along with 8-bit music playing in the background, which resembles the Warp Zone from World 1-2 in Super Mario Bros. Upon entering any of the three Pipes, they will warp the player to certain chapters within the game. Furthermore, finding all six buttons within the first chapter without the use of cheat codes will reveal a rainbow bridge that resembles the Rainbow Road track from the Mario Kart series that leads to a blue Warp Pipe, which takes the player to the secret room.

The second Warp Pipe is inaccessible in the PC version due to the switch used to access it not working; whether or not this inaccessibility was an intentional choice by the developers or a glitch is unknown.