Purchased a disputed plot without knowing

You are a bonafide purchase, but burden lies on you to prove it.  It requires perfect evidence.

The evidense is that the plot has been registered to us and that was witnessed&signed by all necessary parties. The EC shows my name as a current owner of the plot.

Will the agreement holder has any right on my plot? I understood that the agreement holder has right for upto 3yrs on the said property.

What would be the best approach(s) to secure this plot?

file a suit before the court - claiming yourself to be a bonafide purchaser 

most importantly, you have to get a relief from creating any third party interest in the property. 

Thank you. I will approach some local advocate.