Empire from the Ashes

Just a routine day in lunar orbit. That's all Lieutenant Commander Colin MacIntyre, USN, expected. Only a simple training mission to test a new survey instrument intended for the first manned American-Russian interstellar flight.
What he got was just a bit different. First, there was the three thousand-kilometer diameter alien starship pretending it was the Moon. And the millenia-old cybernetic intelligence that shanghaied him to serve as its crew.
Colin might have been forgiven for thinking that those were enough surprises for any one man, but there were a few other small problems. Like the deadly mutiny which had been raging longer than the human race had existed on Earth...and still wasn't over. Or like the millions of other starships, crewed by genocidal aliens dedicated to the extermination of all possibile competing life forms, which just happened to be headed straight towards Earth. Or like the interstellar empire whose aid offered humanity's only hope for survival...except for the minor fact that its last emperor and all of his subjects had died forty-five thousand years ago.
Add in the occasional homicidal terrorist, religious fanatics convinced that the only good MacIntyre was a dead MacIntyre, a bio-weapon capable of killing every living thing on any planet, a super-bomb which could take out whole worlds, a starship drive which could destroy complete solar systems, and the need to organize the entire planet Earth - and all of its warring, mutually murderous factions - for a probably hopeless last-ditch defense, and Colin was convinced that things were just about as bad as they could possibly get.
Until he found out whose job it had just become to fix all those problems, of course.