Click the lever on the right by the door and exit through the door.
When you arrive in the new area exit to your right and drop all four items into the rubbish bin on the wall. Move right (R) and click on the scanner button. Move R and click any four of the zeros on the panel.
At the bottom, go left (L) twice, round the corner, L, L, L and click on the bent grill. Enter the hole.
Move R, up (U), U and pick up the keycard. down (D), L and click on the wheel. R, R move the thing in the middle, and L, L. Click the wheel twice and move R, D, R, through the hole, R.
In this room there are three options you arrived through the bottom hole. Click on the middle one. U, L. There should be two wheels. When you click one it moves a quarter turn and the other a half.
Click the left one once and the right one once. Move R, U, U, click the button and go D, D, L. Left wheel once, right wheel once. (This will get you to a secret area, to access go R, D, R, bottom, L, L, D) Back with the wheels, right once, left once, move R, U, U, click the button, D, D, L. On the wheels, click the right then left. Finally move R, U, U, U, R. Put your keycard in the slot and press the button, move R into the lift.
There are three buttons, click the top one (floor three), move L and click the panel on the wall. Click all three circles and exit the screen (click on the bottom). Go R and to floor two. L, L, L pick up the box (another secret can be found here, on the screen behind make a square of 1s around the center, then go R, R, R, bottom floor, L, L, L, L, D, D). From this secret location there is a long bit of movement.
U, U, R, R, D, D, D, D, R, U, U, click wheel, D, bottom hole, click both levers, L, Middle, R, R, R place box on the plinth. L, click the egg timer, R.
Click on the contents of the box, L, egg timer, R, and pick up the connection pod, L click the egg timer, L, L, L, U, U, wheel, D. (You can pick up 2 more secrets here - bottom, L, L, L, L, L, round the corner, click on thoth, round corner, R, R, R, R, round corner use pod on the rusty machine. click on the pod when you've finished.)
From the room before we branched to get these latest secrets, move middle, U, U, U, U, R, R, floor three, L, L, place pod in the wall. U, disable, D, R, pod. Then R, R, floor two, L, through door, pod in wall, D, disable, U, L, pod. D, R, floor three, L, L, through door.
R, R, R, R, use pod, L, disable, R, D, get pod. L, L use pod R, R, disable all four, L, L read message. D, click pod. (The final secret can be accessed from here - L, L, L, use pod, D, click) from the previous point, R, R, use pod, U, click the box with 'e' in the middle twice. D, D, get pod, R.
Another lift, this time the buttons are sideways and we came in from the left most one. Click the middle one. L, U, pod. L, disable, R, D, disable, U, R, get pod, D, L, U, pod. U, L, disable then quickly cancel (before it finishes or you have to repeat disabling the turret again), yes. R, D, L, get pod, D, R, R, rightmost button, L, U, U, pod, click.
Now we are in the mainframe. L, join the connections by moving your mouse. R, Click the middle twice, R, U, disable, D, R, disable, L, L. Click the middle thrice. U, U, click.
There should be five points. Protocol 1-32, disable and return. 1-28, drag to make the connection, return. 1-35, use your mouse movement to make the connection, return. 1-12, R, reset, yes. L, L. 1-0, U, disable, yes.
D, D, get pod. L, click on cover, click on fan, click on hole, U, U, U, U, R, R, R, use pod on portal, enable.