Enigma codes can be collected from the bodies of commanders you kill. By the time you are able to use the Enigma Machine for the first time, you will have been able to collect roughly 20 codes. These codes are used to discover the locations of Ubercommanders, which open side missions to find and kill them.
The Enigma Machine can be found in the Helm of the submarine, Evas Hammer. It's not accessible until
IMPORTANT: If you don't complete the minigame correctly you will lose enigma codes. Create a manual save before using the Enigma Machine so you can revert back if needed.
Select an Ubercommander you want to track, which consumes varying amounts of enigma codes.
You then need to use the thumbsticks to create the highlighted code. In the example below, you need to create the leftmost code labeled 01. Below are two smaller rows. The left thumbstick
moves the top and the right thumbstick
moves the bottom. You need to move the thumbsticks left and right to match the code that's highlighted and then press
before the timer runs out. The next code is highlighted and you repeat the process until you've matched all seven codes.
Once complete, you can check the map in the center of the room to see the Ubercommander's location and the option to travel there, which starts the side mission. You will likely also get the following achievement for traveling to a district: