I Have not Received Salary so Decided to Left

It is good that you have mentioned it'Please allign someone for Project related Handover.' 

Have you ever apologised in writing?

Was any stinker/memo/SCN issued?

 

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No Sir, I have never apologized in Mail.
No Sir, I have never received any memo from company.

I got such mail, only after submission of my resignation.

Also in the mail, they have written

You are making your exit more critical.
...... From this line we can assume the consequences..

Also if company thinks, I am not doing the job, then what is the need to serve the notice period. By that means they can terminate me. Is not it contradictory.

Please suggest, what is to be replied after the last mail from management.

On said project and said completion until or unless your docs are examined by a very able counsel, wait to draft a reply.

Let your counsel(s) suggest you.