Cannot start Oracle Enterprise 13C after stopping OMS
After all the searching, I could not find any help, until I figured out the problem myself. In order to use enterprise manager, the pluggable database container must be accessible and open before starting the oracle management service.

This can be done through enterprise manager 12C:

Access your pluggable database containers shown below



You will see that container database is down by open-mode column. Click on actions and say open all or the one you want:



Choose the appropriate action(s) to open your PDB's



Or you could run the below query to open all pluggable databases from sqlplus [I tried it from sqlplus and it did not want to work for me]:

alter pluggable database ALL close IMMEDIATE ;
alter pluggable database ALL open read write;


If it works you should see the open-mode in green shown below in enterprise manager 12C:



After starting the PDB, you should be able to start the Enterprise manager 13C OMS as shown below:

#!/bin/bash
export ORACLE_HOME=/u01/app/oracle/product/12.2.0.1/db_1
export OMS_HOME=/u01/app/oracle/middleware
export AGENT_HOME=/u01/app/oracle/agent/agent_inst

# Start everything
$ORACLE_HOME/bin/dbstart $ORACLE_HOME

$OMS_HOME/bin/emctl start oms
$AGENT_HOME/bin/emctl start agent