Before a mission can begin, the crew has to know what their mission is in the first place! At very least, they should be given an explanation of what they are going to be doing. Explaining what capabilities their ship has, which country the crew represents, basic stellar geography (other alien races they might encounter, where their ship is currently located, etc.). The crew should at least have context for what is happening when their mission begins.
Except in very rare circumstances, every mission has a briefing associated with it. The briefing should be included in the mission in some way. The best Flight Directors deliver the briefing without notes, but slides or tactical screens can be used to illustrate. If slides or tactical screens are not available, the flight director should illustrate the points of the mission using a whiteboard or by drawing on paper. Every effort should be made to help the crew understand what they are doing.
If possible, the mission briefing should very clearly outline the mission objectives. These are the key, critical points of the mission which must be accomplished for the crew to complete the mission successfully. By outlining the points of the mission one by one, the crew is much more likely to remember what they are supposed to do during their mission.
This time should also be devoted to assigning the crew their positions. The Flight Director should be well aware of what station set the simulator is configured to use before the briefing begins so the crew can be given the appropriate positions. If available, uniforms should be distributed. If the crew isn't already on the simulator, they should be escorted to the simulator.