I remember this game, it's awesome. I don't remember the code, but the internet does (as well as how to figure it out):
THE SECURITY DOOR: First use an infra red scan on the keypad. This will display a reading of heat from the previous person to access the door. The keys are cooling off in the order in which they were touched, allowing you to read the combination, which is 2571. After punching in the code, press the enter key on the keypad to open the door.
There's another part where you need a code to close a door, and you get that from a computer somewhere else:
THE ELEVATOR PUZZLE: You must have a code to close the elevator doors to prevent being killed by the blast grenade. The code is at the H. Suzuki computer terminal. You will find dossiers for the people who work in the complex. A temporary access code has been given to a new employee who is the last record in the terminal. Obtain the code and return to the elevator. Enter the code quickly to avoid being killed by the grenade. To enter the code correctly, you must repeatedly press the buttons to cycle through the available choices.
The Halon system was a gas chamber:
GUARD BEHIND GLASS WALL: You will find yourself in a storeroom on the lower level of the complex with a guard behind a glass wall. If he sees you he will activate a Halon System and flood the room with poisonous gas. You must sneak past this guard. Watch his cycling movements from the computer terminal to his notes. Sneak past him when he turns away from the window. Once past him, take the door out into the corridor. The first door on the left is the room he is working in. Enter the room and kill him.