What is a good way to start Data Analysis of unknown dataset (JSON data)
@Emre makes a great point. You should probably ask the business what they're trying to accomplish because only then will you know which data matters. You don't want to waste time cleaning up data that has minimal importance to the business. 

Regardless of the business objective though, it's worth pointing out that Mongo DB is a pretty poor choice for storing analytical data. There is no enforced schema, so each record might be in a completely different and unexpected format. You might have entire columns missing, maybe no columns at all, wrong data types, duplicates, and no way to get easy summary statistics like you would in a relational database. You're pretty much going to have to do a database dump of your MongoDB data and probably comb through your records semi-manually, looking for commonly occurring schemas and going from there. 

Summary: MongoDB is great for operational data when all you want to do a quick lookup. It's a poor choice when you want to do any sort of in depth analysis on it though. Relational databases are better for analytical queries because the data is structured and also because you can more easily enforce data quality.