It may take several minutes to shut down the system. Be patient, and do not try to quit the process with ^C. When completed, the entire system, with the notable exception of extra hosts and vaults that were started separately (see section 7.0 in the Basic User Manual), will be deactivated.
If you have enabled security, the shutdown process is complicated. If you are using a PCD host as your bootstrap, it is very complicated. There is no "root" user and each user owns his or her own objects. We suggest that you avoid trying to shut down a secure system with a PCD bootstrap host unless absolutely necessary. Please contact us at email@example.com if you have any questions about this.
If you have only one user (i.e., /users/admin) and are using a basic host object on your bootstrap host, run legion_shutdown while logged in. You will probably need to clean up after the system by hand (i.e., kill the processes one by one from the command line: you can use ps to check that all Legion processes have been killed).