In its developed form the Enigma machine had a keyboard, plugboard, three or four rotors, and a lamp table. |
After the smoke cleared, he ran his program on the Codebreaker II and found that it did, in fact, figure out the correct settings, including the plugboard. |
A common approach was to input the program by some physical means, such as wiring a plugboard, and then feeding in the data for the program to act upon. |