Conversion of capital asset into stock beyond the objective

Case : X company carrying the business of cotton converted a plot of land which was held as capital asset into stock in trade and sold it in smaller plots (layout) .These transactions were completed two years ago.such sale resulted in capital gain. company has not filled its return of income since these transactions took place. what could be the tax consequences.does the conversion result in real estate business. if yes whether it could mean that company has carried business which is not mentioned object clause of MOA. Does this transaction mean entering into ultra virus transactions beyond the capacity of company.if it is beyond the capacity of company, the transaction is invalid , if the sale is invalid naturally there should not be any capital gain. this case was illustrated form a real case. please suggest a way out