Stopping a program before it has run its course and reached its natural conculsion - being that all contacts have either been Handed Over to you for manual management or have been Retired for one reason or another - will stop all future planned automation regarding the conversations with those contacts. If any contacts remain Status:Pending (meaning they have not yet entered the programs main outreach sequence) they will not be entered into the communication flow.
NOTE: Stopping a program is generally not advisable (unless really required) because depending on when you stop the program, you could end up with a large number of conversations that you may then need to manually manage in order to continue progressing the dialogues.
Should you decide to stop a program, you will receive a closing report (via email and via the program details page for the specific program) detailing the status of contacts in the program and how far along contacts were in the automated journey. You will then need to decide what to do with the contacts in order to progress or close the conversations. Any contacts who are Status: Progressing when you stop the program will become Handover actions which you will then need to takeover and determine what to do with.