If you have built MySQL from source code and replaced the built-in InnoDB in MySQL with the InnoDB Plugin in the source tree as discussed in Section 9.4, “Building the InnoDB Plugin from Source Code”, you have a special version of the mysqld executable that contains the InnoDB Plugin. To “uninstall” the InnoDB Plugin, you replace this executable with something that is built from an unmodified MySQL source code distribution.

Before shutting down the version of the MySQL server with built-in InnoDB Plugin, you must enable “slow” shutdown:

SET GLOBAL innodb_fast_shutdown=0;

For the details of the shutdown procedure, see the MySQL manual on The Shutdown Process.