Story mission cannot be missed.
Its the mission that starts after the "altered not allowed ceremony" and your forced sleep. You wake up and you are told that your doctor picked "the black stone" and is now taken by the Enclave doctor to their secret base. You go after them, as usual, fight some enemies, get to the 2 doctors, watch the cutscenes, experience some surprises, fight your way out, exit the mission area and it should pop.
No spoiler tags uses as I hope I did not reveal anything essential. :)