Deus Ex/Majestic 12 Prison

Prison
Shortly after you arrive in the prison, Daedalus will contact you and open the prison door for you.

Your cell is guarded only by one MJ12 trooper, and you have immediate access to a baton and a combat knife. The cabinet contains two multitools (one of which is locked).

If you want help, you can open the cell doors using the code 4679 (as found on the table). You can use this for medical help as well as to recruit Miguel.

The MJ12 base has a large number of ventilation shafts that can be used; this allows bypassing guards as necessary.

Robot Maintence
In the top floor (accessible on the right), you can enter the upper offices. After dealing with the troops, you can reverst the targetting AI of a robot and have it defeat the enemy MJ 12 soldiers.

Armory
As you can discover in the Robot Maintence office area, the code to the armory is 2971. It is guarded by two heavy military robots that are strong and capable of shooting rockets.

When you enter the armory, and disable the security, you can recollect any desired equipement. Your stuff is located on the shelves, and there are other weaopns available to collect if desired.

The computer contains the passcode for the plasmagun container, which is 5283.

Medical section
The medical section is to the north. En route, you can find Dr. Monreau who gives the code 0199. When you reach the medical bay at the end, Daedalus will give you the exit code 1125.

Command center
The command center is the large circular area in the middle, near the prison. It has a few MJ12 guards and dogs. While you can shoot the glass for a shortcut, it will set off the alarm.

When you have the access code, enter 1125 to exit. You can sequence break simply by entering the code directly without the preceding contact with Paul.

Unatco
When you exit the MJ12, you will enter the basement of Unatco. There are several people you can speak to:
 * Jamie Rayes is friendly, and if contacted, can be given a choice between being a spy for Unatco (allowing to instantly defeat a later enemy) or to follow you to Hong Kong.
 * Alex Jacobson is friendly, and gives you the key to the front door as long as Anna Navare is killed.
 * Sam Carter will unlock the armory for you.
 * Shannon is in the break room. She will sell scramble grenades for 1250 each.
 * Joseph Manderly is in his office speaking with Simmons. While he remains passive while you speak with him, he may shoot you in the back as you leave the office; his bullet can kill you in one hit.
 * Anna Navarre, if still alive, is at the front entrance on level 2. If you can't defeat her directly, you can obtain her kill phrase by hacking two computers; the one in her office (located across from the armory) and the computer in Manderly's office. If you want to keep her alive, throw a gas grenade from the lower floor to trick her into opening the front entrance.

Head to the front entrance and head to the helipad. If you didn't buy scramble grenades, you can collect one from the Satcom van before leaving.