There are two place which "store" data in Hyperledger Fabric:
1. the ledger
2. the state database
The ledger is the actual "blockchain". It is a file-based ledger which stores serialized blocks. Each block has one or more transactions. Each transaction contains a read-write set which modifies one or more key/value pairs. The ledger is the definitive source of data and is immutable. The state database holds the last known committed value for any given key. It is populated when each peers validates and commits a transaction.
The state database can always be rebuilt from re-processing the ledger. There are currently two options for the state database: an embedded LevelDB or an external CouchDB. As an aside, if you are familiar with Hyperledger Fabric channels, there is a separate ledger for each channel as well.