I read this series about 10-15 years ago. It starts out with a manned flight around the moon. The ship then brings him in and he ends up being made the ship's captain by the computer. It turns out that the "Moon" is really a ship that has collected a great deal of rock and dust for several millennia.
He then goes to the "Navy Headquarters" to find that the everyone is dead and then ends up Emperor by mistake.
This could be Empire from the Ashes series of books by David Weber, originally published in 1991.
You can read the first book in the series (Mutineer's Moon) for free online here
"For Colin MacIntyre, it began with a routine training flight over the moon. For Dahak, a self-aware Imperial battleship, it began millennia ago, standing guard against an unknown enemy which once devastated the galaxy-and now has returned. So Dahak grabbed MacIntyre's ship and informed him that he was drafted to be its new captain and lead the fight against the ancient enemy.
The moon is a moon-sized spaceship
"It's not possible," MacIntyre said stubbornly. "If this thing is the size you say, what happened to the real moon?" "It was destroyed," his informant said calmly. "With the exception of sufficient of its original material to make up the negligible difference in diameter, it was dropped into your sun. It is standard Fleet procedure to camouflage picket units or any capital ship that may be required to spend extended periods in systems not claimed by the Imperium."
"You camouflaged your ship as our moon? That's insane!" "On the contrary, Commander. A planetoid-class starship is not an easy object to hide. Replacing an existing moon of appropriate size is by far the simplest means of concealment, particularly when, as in this case, the original surface contours are faithfully recreated as part of the procedure."
He's made Emperor as part of an attempt to hack into a battle computer;
"Damn it. Damn it! We need an emperor to get into the goddamned system, and the last > emperor died forty-five thousand years ago!" "Captain," Dahak said after a moment, "I believe there might be a way."
"Colin screamed in the grip of an agony too vast to endure, and yet it was over before he > could truly experience it. Its echoes shuddered away down his synapses, stuttering in the racing pound of his heart, and then they were gone. "Case Omega executed," Mother said emotionlessly. "The Emperor is dead; long live the Emperor!" "
I believe this might be mutineers moon, by David weber
http://www.goodreads.com/book/show/1107296.Mutineers_Moon
The top line description from Wikipedia is - The book’s premise is that the moon is a massive space ship controlled by a self-aware computer that wants its rightful crew back aboard.
It is part of a series of books and 'mutineers moon' is the 1st in the set, it is now available to read on line for free at the baen free library
Www.baen.com
