Dispute regarding cheque bounce and company

I am an engineer and basically doing research on fuels. A year back I came in contact with two people X &Y from Sonipat who offered to fund my research for the purpose of setting up an industry. Intially they promised Rs.10 lacs .They transferred Rs.5.5 Lacs from their personal account to my wife’s and brother account.

We also formed a company with me and Mr.X being the director with 40 and 60% shares respectively. Two months back they started asking me for the money and threatened me. I had also sent the machines to their factory. I have filed a case against them.However I had forgotten that they also had one of the blank cheques of the company signed by me with them. The bank account is operated jointly by me and Mr.X. Mr. X misused the cheque by making it bounce by showing a payment of Rs.21.5 lacs against one of his friends.

He also made himself one of the accused. Now a legal notice under Sec 138 of NI act has been served upon me and it has been alleged that a friendly loan had been given to us by the complainant while no transactions of this magnitude has been done. What am I supposed to do now?