There are two ways in which you can proceed. Agree to whatever the Company says and get a good certificate. It should be such a certificate that they should not be able to go back on it. Join another good company and forget the past.
Second option is "fight". Women's commission or a good women's NGO should be able to help you. They will advise you what are your legal rights and how you can go about it. You can file an FIR with the police. Generally the police will prevaricate on filing FIR. But if the women's organisation intervenes the police will act. Who is your lawyer at present. Is it a lady or a male. The women's organisation will help you to get a competent lawyer. I warn you that the fight can be long and arduous. Is your complaint of harassment against a particular person or are there more than one person? Is the person high up in the hierarchy or was he approximately at the same level as you? In which place are you and in which place is the Company? In what business is the Company engaged?
Please note that I do not recommend any particular option. But the two options are mutually exclusive. You have to make the choice.