I only remember bits and pieces hopefully someone will
recognize this story:
The main character is on a space ship (maybe part of
security) and somehow helps save the ship or other
ships (he is able to sense and see things beyond
what the ship sensors sees). As he does more this the
crew begin to fear him. He and the captain agree
that he need to leave the ship.
He leaves the ship with a few people and he begins
to learn & expand on what he senses as he explores.
Along their travels, they find a planet where all
the people are gone but the building and structures
are still there. Some race has remove all the people
from the planet for some reason.
He builds a big ship that has lots of room and more
and more people/races join him. He also keep
increasing the technology he has to help protect
all of them.