First stop all process (make sure with ps -ef, if not the drop will fail)

Stop the agent and OMS

/u01/app/oracle/agent12c-u4/core/12.1.0.4.0/bin/emctl stop agent

/u01/app/oracle/middleware/oms/bin/emctl stop oms -all

Then drop the DB

cd /u01/app/oracle/middleware/oms/sysman/admin/emdrep/bin

./RepManager emdb1.domain.com 1521 OEM -action drop -dbUser sys -dbPassword password -dbRole sysdba -reposName SYSMAN -mwHome /u01/app/oracle/middleware/ -mwOraHome /u01/app/oracle/middleware/ -oracleHome /u01/app/oracle/middleware/oms/