Long leave on without pay in psu

Hello Sir, I am working in one of the PSU as an engineer. I was on leave on without pay since 1.5 years because I was in the depression at the time (because of some of my personal and some of the family) and later caught by jaundice and typhoid in that period. (Prior to this I also took 5 months leave for higher study which is not sanctioned though they accept me when I went to join the organization.) Recently, I got the letter from the disciplinary authority and they are stating the charges of misconduct and loss to the organization because of me. I also sent the resignation letter in the month of Dec'17 prior to this proceeding but it did not reach to the organization (I do not know why?). I have to reply it within 15 days which I did by attaching the xerox of my resignation letter but now they are asking about the charges they frame. Not accepting my resignation letter though they did not say anything in the letter about my resignation. Can you please tell that what are the options I have? What I have to reply to them now? What kind of actions can they take? Does this affect my future employment?