1.Your all original documents with them.
2. If you signed any document means that will come under to process any legal activity from Employer.
3. better to do mutual understanding with them and come out of that.
4. if they will accept any payment lieu of agreement breach, then process it.
First & Important part over here that, as you said, company is not register under (Ministry of corporate affairs), Means, it is register under which act...? whether it is Pvt., Ltd, Proprietorship, Shops ..?
Who has signed the agreement or offer letter as representative of company..?
My comments on your issue without reading any document of you, are as under:
1. Normally I avoid making comments in any legal issue without reading all the relevant documents fully and carefully;
2. Prama facie it seems to me that the contract between you and your employer is illegal;
3.It is illegal on the part of your employer to keep your original documents with him and do not return;
4. Your employer can not blacklist you but you can blacklist him with NESSCAM. NESSCAM is a body of association of IT employers;
5. Every employer is not required to be registered with MCA. Only Ltd., Pvt.Ltd. and LLP are required to be registered with MCA;
6. You are advised to approach a good lawyer with all your documents pertaining to your employment and serve a legal notice on your employer;
7. I would have not advised you to spent your time, money and energy in serving a legal notice on your employer but since your original documents are lying with him, you have no option.
Wish you all the best.