First of all, I liked it... I'm a sucker for time-travel stories and I think this one survives the initial round of "WTF?" thinking that such a story always brings on... And to be clear, I think Adam and Eve starting the human race is a time loop and not a paradox. A paradox is going back and shooting your Grandfather before your Father is conceived, while a loop is going back and actually becoming your Grandfather. (ewwww) A paradox usually implies some sort of impossibility, a loop is just hard to grasp.
My vision of these races' themes would largely follow Avatar's, that is, Ancient Hadean ships are tan-ish, colored like many artifacts in BZ1. Hadean ships are asymmetrical and lustrous, yet centered around even numbers, and have thematically/primarily blue and green homing missile like projectiles. Olympian ships are black, red, and orange. They are symmetrical and rugged, but centered around odd numbers, and have thematically/primarily red and orange laser and blast like weapons.
I'll over look the reversing of the Ancients, as the Olympian artifacts are gold and shiny while the Hadean artifacts are black and red, not the other way around. No big deal, just switch sides of the planet.
I'll offer a few suggestions:
The ship passes through the moon, and yes the 'spacewarp' drive bit warps the moon around the ship but causes massive damage in the process. Coming out on the other side it's immediately apparent that the ship is done for and the order is given to abandon ship... the incoming attack waves are just icing on the cake and a good example of Murphy's Law in action. "Could be worse... could be raining!" (cue thunder).

As to why it happens, there are a lot of ways to explain it.
Maybe the Hadeans and Olympians are doing wormhole experiments of their own and space is warped in the vicinity of their planet, throwing off the ship's instruments.
The ship is also, after all, the first of it's kind and maybe it's just not up to the task what with the experimental instruments and drive and all.
The ship could be time shifting the whole time the drive is active and the moon simply wasn't there a minute ago.
Love the approaching moon bit... love it! Very dramatic and the best motivator known to man.
Abandoning ship consists of boarding the already packed Dropships and scattering to escape the incoming attackers. Each Dropship already holds a mixed bag of Tanks, Troops, and a Recycler. The escaping ships land at various places along the twilight zone, with many of them being destroyed in flight. After this mass exodus some join up with Hadeans, some with Olympians, and it's up to the Player and his missions to sort it all out. Guarding the Dropships will be necessary given the ending, as they'll be the only way through the wormhole.
Going through the wormhole at the end means hopping back in a Dropship and heading out. Going through could also determine 'when' you come out the other side. If Adam and Eve are the very last ones to go through it could be that the approaching moon warps the wormhole, and they end up waaaaaay back in time, much further than the other forces that went through earlier. You could have the wormhole flickering, warping, and changing color to indicate this. This is why they're back before the Hadeans and Olympians, before the planet is habitable, and able to seed the beginnings of life on Earth. The warping wormhole could also be why their ship is trashed, and they could even leave it in orbit when they discover it's inoperable, something for the future Hadeans and Olympians to discover.
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I have, btw, both Ancient Hadeans and Olympians fully operational although not completely done. I plan on using a lot of DLL help to make them interesting...

I have some maps made as concepts for the Hadean and Olympian parts of the planet, but no missions scripted yet. I have missions outlined in Word, but nothing coded.
I don't see this story as conflicting with my ideas all that much, as it takes place so far back in history compared with my own intended stories.
I don't know how to explain them having biometal, and then not having it so that Nexus can invent it as stated in their records found in BZ1. Maybe they don't actually know how to make their own but are using the huge amount that fell from the Ark III? Maybe they devolve into savagery when they get through to Icarus and have to start their civilization all over again? Losing their history and technology for a few hundred or thousand years adds a bit of flavor to the story anyway...

Good work for a mod start... simple enough to work with but interesting enough to allow for a lot of options.

-Av-