Manager has filed false data integrity case on me - how to reply to legal notice?

I work with a US firm located in Manesar, Gurgaon. And my manager has filed a wrong data integrity case on me.
The case was filed on 21st may 2018 and nothing was found to prove me guilty tll now. I met with HR for several times in between for investigation. It's been more than 4 months now.
Today HR called me and gave written complaint on company letterhead as said me it was informal till now and now it's getting just formalised. HR took my laptop and said that till the time investigation is going I will be on paid leave.
I don't understand what is formal and what is informal inquiry. My question is when the case was filed on 21st May, then why I am receiving the legal complaint now?
I need to reply them and need some help from someone who has legal background. Kindly help as I have to reply by 1st Oct 2018.
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