Ok I've been trying to find the name of this really old anime I remember from back in the 90's. For the majority it took place in space, and was an all female crew, except for the last little bit. The basic plot was that the crew had a mission to protect some "precious" cargo against their sworn enemy. The sworn enemy wore some clothing that covered their body so you couldn't see their face. I can only assume from the overall plot that the enemy was an all male alien race.
The "precious" cargo eventually gets opened and its a baby boy who starts growing very quickly. It basically ends when the spaceship crashes on an alien planet. There's a little more afterwards, but its basically the interaction between the boy and the females. It cuts into the future at one point and you see a world populated by people that look like all the survivors, I'm assuming its supposed to mean that the boy and all the girls procreated and recreated the human race.
I also found this while doing a search for it, http://www.animeforum.com/archive/in...p/t-63370.html
I can't remember if all the details the OP recalls are correct, but it seems to be the same anime I am remembering.
If I remember correctly the title had something to do with "Genesis", possibly containing the word "Project"