After training is completed and the crew is familiar with the controls the mission can begin.
Flight Directors commonly play as a Main Computer to the simulator (or another similar AI unit unique to the simulator) and have the mission begin when that system "activates". The startup introduces the AI system and the ship identity. (Ship name, registry number, and class.) The ship controls will then need to be reset from training mode to what is referred to as "Operational Mode".
Reset the flight and the crew is good to go. Take a moment to send introductory messages through the internal messaging system, send an intro long range message, have maintenance of some kind or a minor broken system , and send sensors data explaining the ships current location/condition.
A common procedure is to have the ship "docked" after resetting. By giving the crew a list of undocking/launching procedures, they can practice using the stations before the stress of the rest of the mission begins.
With a larger station set it can be helpful to have a voice actor as an officer on a lower deck who can give helpful suggestions throughout the mission as necessary. If the FD wants to have a character like that, it is recommended to have them say hello and introduce themselves to the crew at the beginning of the mission before the crew heads underway.