Salary file, scrutiny

First of all the ITD might issue a notice u/s 142 for non filing of IT Return. In response to it if you file the return within the prescribed time by the Dept., then your return may get processed by the dept. But if the dept. feels that more clarification is needed, then scrutiny might be opened by the dept. that too by giving sufficient chance to the assessee for explaining the reason that why the return was not timely filed.

It is merely failure to file the ITR, as he is a salaried person, the tax that is payable to Govt has been paid through TDS. 

As @ Vimal said, the ITD will send notice u/s 142. As you have filed a condonation of delay, the AO may also let you file the return. 

If the department finds any deviation in the income or tax to be paid, then it may call for scrutiny.