Awesome idea, do it. Maybe she shouldn't call them aliens, or have any direct mentioning of them being aliens, just like MM. It's just alluded to heavily, and space ship / mini dungeon would be a great idea. Even have a small boss type fight, nothing huge, that'd be sweet. Alien leader type dude 
Well thanks Malefor for the inspiration. Now that I see others also like it I'm gonna see if I can't come up with some dialogue for it.
@Blaze, it isn't exactly 100 years before MM. and Cremia and Romani don't even have to be the same ages as in there. I may not even use both of them, I don't know yet.
Alien leader type dude who... maybe spawns more aliens? Or maybe you have to destroy certain objects in his ship before you can hurt him. I think it could work a few different ways as a mini boss fight.
1- Destroy stuff while dodging traps, attack him. He summons minions, kill minions, attack him. He summons minions while using a ranged weapon every now and then. Kill minions, attack him. Win. He zaps Link and Dark Link back down to earth with a reverse tractor beam before blasting off into orbit in his ruined ship.
2- He uses some sort of coil things for energy. Each one requiring a different item from a dungeon you've completed to either reach or destroy. He starts off shielded. Destroy one coil, attack him. He recharges, teleports, and you repeat. Each time he gets faster and begins to teleport more frequently making him harder to hit. Which could make your and DL's placement more strategic if you want to make it easier.
3- He doesn't fight you at all. he sends a crapload of aliens after you.
4- He doesn't send aliens. He simply attacks with a ranged weapon and teleports frequently.
(An alternative to being teleport zapped out of the ship, Link could be simply blown out of it, landing unconcious in the ranch somewhere. I could completely imagine him crashing through the roof and landing in that hay pile of the barn. It'd be funny and cool to have a hole in the roof for the rest of the game.
If any of you have ideas then feel free to share them. I want this game to be one of the best fan games out there. And well, it could turn into a community made fan game which would be awesome for me, my team, and this site if it becomes popular.
I just keep getting IDEAS!!! So how's this...
I can make Dark Link also have a side story, I'm not sure yet what you'll have to do but I'm thinking he can unlock a different bonus for each one. Maybe him regenerating health in darkness doesn't have to be a default ability, but instead it can be the first one you unlock for his side story. Which can start as early as right after you get the sword. I'm thinking I could have them work similarly to finding photograph spots on LA. Where there are event triggers depending on where you are. Except these won't be indefinitely missable. Maybe these spots could be his favorite areas or spots that hold some sentimental value to him. These abilities would only serve to make him a more reliable partner. So he could... regenerate his darkness powers faster, regen health faster, move faster in dark areas, become invulnerable while blocking, etc.