ERROR 1054 (42S22): Unknown column 'plugin' in 'mysql.user'
Your problem has to do with mysql.user and the way you upgraded to MySQL 5.6

If you look my answer to Cannot GRANT privileges as root, I show you the description of mysql.user from MySQL 4.1 to MySQL 5.6.

The column plugin is column #41 in mysql.user in MySQL 5.5/5.6

mysql&gt; SELECT column_name,ordinal_position FROM information_schema.columns
    -&gt; WHERE table_schema='mysql' and table_name='user' and column_name='plugin';
+-------------+------------------+
| column_name | ordinal_position |
+-------------+------------------+
| plugin      |               41 |
+-------------+------------------+
1 row in set (0.04 sec)

mysql&gt; SELECT version();
+-----------+
| version() |
+-----------+
| 5.6.24    |
+-----------+
1 row in set (0.02 sec)

mysql&gt;


That column does not appear in MySQL 5.1, 5.0 or 4.x. What this tells me is that somehow MySQL was upgraded to 5.6 but still has the mysql.user from 5.1 or older.

If you run SELECT COUNT(1) column_count FROM information_schema.columns WHERE table_schema='mysql' AND table_name='user'; and you get 39, I have just the fix for you.

See my post MySQL service stops after trying to grant privileges to a user on how manually fix mysql.user from 5.1 straight to to 5.6.