MySQL broken, databases deleted - mysql

Question

I use MySQL 5.6. One time my server was suddenly stopped. MySQL is not starting now. In the folder where databases folders and files was stored - all folders was disappeared and only folder "WARNINGS" is there. When I try to start mysql I am getting the next log:
2018-09-21 03:02:31 0 [Note] c:\ospanel\modules\database\MySQL-5.6-x64\bin\mysqld.exe (mysqld 5.6.38) starting as process 4600 ...
2018-09-21 03:02:31 4600 [Note] Plugin 'FEDERATED' is disabled.
c:\ospanel\modules\database\MySQL-5.6-x64\bin\mysqld.exe: Table 'mysql.plugin' doesn't exist
2018-09-21 03:02:31 4600 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2018-09-21 03:02:31 4600 [Note] InnoDB: Using atomics to ref count buffer pool pages
2018-09-21 03:02:31 4600 [Note] InnoDB: The InnoDB memory heap is disabled
2018-09-21 03:02:31 4600 [Note] InnoDB: Mutexes and rw_locks use Windows interlocked functions
2018-09-21 03:02:31 4600 [Note] InnoDB: Memory barrier is not used
2018-09-21 03:02:31 4600 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-09-21 03:02:31 4600 [Note] InnoDB: Not using CPU crc32 instructions
2018-09-21 03:02:31 4600 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2018-09-21 03:02:31 4600 [Note] InnoDB: Completed initialization of buffer pool
2018-09-21 03:02:31 4600 [Note] InnoDB: Highest supported file format is Barracuda.
2018-09-21 03:02:31 4600 [Note] InnoDB: The log sequence numbers 633063664 and 633063664 in ibdata files do not match the log sequence number 633063674 in the ib_logfiles!
2018-09-21 03:02:31 4600 [Note] InnoDB: Database was not shutdown normally!
2018-09-21 03:02:31 4600 [Note] InnoDB: Starting crash recovery.
2018-09-21 03:02:31 4600 [Note] InnoDB: Reading tablespace information from the .ibd files...
2018-09-21 03:02:31 4600 [Note] InnoDB: Restoring possible half-written data pages
2018-09-21 03:02:31 4600 [Note] InnoDB: from the doublewrite buffer...
2018-09-21 03:02:32 4600 [Note] InnoDB: 128 rollback segment(s) are active.
2018-09-21 03:02:32 4600 [Note] InnoDB: Waiting for purge to start
2018-09-21 03:02:32 4600 [Note] InnoDB: 5.6.38 started; log sequence number 633063674
2018-09-21 03:02:32 4600 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
2018-09-21 03:02:32 4600 [Note] - '0.0.0.0' resolves to '0.0.0.0';
2018-09-21 03:02:32 4600 [Note] Server socket created on IP: '0.0.0.0'.
2018-09-21 03:02:32 4600 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist
I have been trying mysql_upgrade, mysqld --initialize-insecure it doesn't help me.
My script feature is it running 16 threads 24 hours per day without stopping. So 16 connections are connected to DB everytime.
On mysql configuration I have set:
interactive_timeout=31536000
wait_timeout=2147483
And nothing more unusual.
I have this situation second time, when the DB was broken.
I want to know, why do I get this problem and how to solve it.