This secret is located in Chapter 4 - The Awakening - Part E. Through this level there is a series of three buttons which much be activated in this order...
Button 1 - In the room with the three shock troopers the first button, as you enter the room, is on the back of the right top portion of the area that holds rocket launchers in about the middle. You may have to tilt the camera upward to see this area. Destroy the black object to reveal the first button.
Button 2 - In the room after you fight the two Seeker Elites, go to the locked door and do a charge jump to the area above the door. There is a button on the ground all the way at the end of this area. Destroy the black object first.
Button 3 - Right before you meet up with Enorym in the room with the dead Aurelian. Jump to the bottom, below the platform, and go to the furthest column in the back to find a button behind it.
Backtrack to the previous room, and a new door is unlocked. Go inside to find the Advent Rising staff room complete with pictures of the AR staff by each console. Activate the consoles inside the room in this order to get an image of a ninja wailing on a guitar in the middle of the room...
Console 1 - guy with the white guitar
Console 2 - guy with the black-rimmed glasses
Console 3 - guy with the wooded background
Console 4 - person with the long black hair
Console 5 - guy with mustache and beard
Console 6 - guy holding up the "Utah County Sheriff" sign
Console 7 - guy with spiky hair and glasses (Donald Mustard)
A Mario tube has been place in Chapter 1 sec. B. You will have to play through to the area where you are standing on a balcony overlooking a courtyard. If you jump down your game is restarted from the last checkpoint. Acouple of thing must be done first.
One, go to the cheat menu and click on Blizzow. This will give you all powers. Two, go out onto the balcony and get up on the edge. This is done by walking out the door and going forward until you climb up onto the ledge. Third, pick the Timeshift ability from your powers menu on the D-pad. Fourth, face towards the ramp on the upper platform. Fifth, move forward, jump and press the Timeshift ability twice. You can press it three times and you will be further onto the platform. Also it helps to look up slightly. This will keep you level. You then want to move to the back and there you will find a ramp leading down to a Mario Tube. Enter this and traverse the moving paltform(easy) and at the end you have three tubes to choose from.
The three tubes from left to right. The fisrt one takes you to the hanger where you get the ship to leave the Earth.
The first one goes to Extinction Agenda chapter 3 part F .
The second tube goes to Extinction Agenda chapter 3 part A.
The third tube takes you to Surface Tension chapter 2 part A.