Resignation vs Termination

Sir, I worked in a very recognised government organisation for 10 yrs.My active service duration was 8 yrs out of 10 years ...I got 1 year maternity leave becaz of having 2 kids and I extended 1 and half year after maternity leave was over. . It was leave without pay ...I rejoined the same organisation after given required explanation. I worked regularly for 2 years without having any loss of pay during that time...it was very tough period for me because of my kids and no body was at my home but I did. One day I got sick and my condition was not good enough to go to office. .this time I required much rest. .on seeing my family circumstances and my health issues I decided not to join office again and I resigned from the Job. I submitted resignation letter but according to organisations policy Resignation is possible through online organisation HRMS Portal. ..but in my case it is found that my leave calculation was not done regular basis ..so many complications arise...so I was not able to resign through proper channel. .after 3 months I was informed that I should go for termination because taking VRS is very long and complicated. Kindly guide me what can I do in my case. .because of those employees who did not calculate my leave ..not done their work...made my leave details complicated. ..which was not sanctioned even timely basis...my colleges. .my manager were responsible for that. .but now I am forced to get terminated please guide me related to my matter