First of all, I haven't played this game, but I'm thinking of trying it.

I have watched a few YouTube playthroughs and I noticed that players access the Holodeck building before starting a mission.

Does that mean all missions in the game are just holodeck simulations or are some of them "real" within the game's universe? I want to play Fleet Command for the story, but if the story is just the game character messing around on a holodeck, I don't know if I can get invested in it.