Go to Kyouju's place in the first section of the street area on Second Miltia. Go down stairs and check the Forbidden Device here. Thanks to the Sequencer A, you can dive into the Sky Ruins which is the third secret dungeon. Defeat the bosses in this area to get to the item chest that contains Decoder 12. Use it to open a red door that's also in the Sky Ruins to get Sequencer D.