Load the clear data and talk with Hakase/Professor that's near. Now talk to Captain 
Mathews and select the second option to get back to Second Miltia to look for Kyouju
(another word for professor in Japanese). While you are Second Miltia, go to the first 
sector of the street area. Now head up the stairs that's near the save and UMN plates. 
Take the room to the left. Enter the room and talk with Kyouju. You will get "Sequencer B" 
and now head to an UMN plate. Select the fifth option which is the Ormus Mobile Fortress. 
At the first intersection, head to the right then up to check out the Forbidden Device. 
Select the first option to dive into an Encephalon. You will be at the first secret 
dungeon where you use your E.S. Defeat the boss in this dungeon and get Sequencer C 
for the next dungeon.