Above Ground

A. Key Card: Get the Key Card here to unlock the main door.

Administration

A. Trapped Employees: You can't go on until you rescue the people trapped in this room. After rescuing them, return here to pick up a Small Medkit.
B. Clinic & Store: After rescuing the employees, you'll go here regularly to buy weapons, armor, and Medkits. You'll also want to visit the doctor, who will heal you for free.

Bio Labs

A, B, C. Environmental Control Switches: Flip these switches to cool off the maintenance area.
D. Secret Weapon: You can't access this room from the main entrance since there's a locked door in the way. There's a secret path much later in the game that will bring you back here.

Maintenance Area

A. Secret Armor: Go to the Maintenance Area entrance in the Above Ground level after you finish the Bio Labs to get an armor pickup.

To solve Maintenance Area, remove the battery from slot D and place it in the slot E. Remove the battery in slot F and place it in slot G. Pick up the battery H, remove the battery in slot G, and then place both of them in slots I. Pick up the battery J, and then remove the batteries in slots I. Place a battery in slot F. Remove the battery in slot E. Place your three batteries in slots D, C, and B. You can now enter Central Processing.

Central Processing

Note that most of Central Processing is arranged in a 3x3 grid. This grid corresponds to the 3x3 grid you see in the displays that are brought up when you press your Use Button on the terminals. The trick is to build a white line that leads from the starting room all the way to an exit.

This image shows the path you need to build to reach exit A. This exit will take you to the Bio Labs for the secret weapon.

This image shows the path you need to build to reach exit B. This exit will take you to the path to the final monster.