A generation ship has two captains, one for the outward, alien
searching trip, and the other for the return trip. Unfortunately,
Captain One has become a dictator, obsessed with finding aliens, and
arranged to suppress the memory of Captain Two. Captain Two's
memories start with a fake memory of being injured and receiving first
aid. He is alive only because Captain One was programmed to not kill
his potential successor. However, Captain One has a long lived son
who could succeed his father (as foolishly pointed out by Captain Two
as he struggles to learn the truth about the past). Meanwhile, the
opposition has been breeding the ship's residents to produce pacifists
who won't obey Captain One's orders. There's a religious ceremony in
which members of the crew have sex with holy women, and only those
people with the desired qualities are fertile.
Captain Two must overthrow Captain One with the help of his pacifist
followers. In spite of that handicap, he succeeds and heads the ship
back to Earth. When it gets there several centuries later, they find
aliens!