BIGGEST THREARDS FROM INCOME TAX DEPARTMENT !!!!!!!!!!!!!

One of my client got a notice u/s142 (1) from income tax department for non filing of income tax return for Ay-10-11, 11-12, ,12-13.

Now I have computed his income and paid  tax accordingly.

but i can not file the income tax return online for same assessment years because period is over. 

 1) what should i do in such a situation? and
 2) how to file return? 

Thanks