The basic premise is sort of like what happened to the Spiral Warriors after they were defeated by the Anti-Spirals, except it happens to the Gurren-dan before they are able to overthrow Lord Genome. The Gurren-dan is defeated, but most of them manage to evade capture and execution. They split up and decide to hide out until the Beastmen have stopped looking for them, at which time Simon will give a signal or come find them all so they can rejoin forces and restart the resistance. Maybe they've managed to hide some of their Gunmen somewhere, so that they're not all destroyed and they have at least some chance later on (definitely Gurren-Lagann at least, because without it they're kinda screwed). But yeah, for now, the main thing they have to focus on is just surviving for that long.
So Rossiu, Gimmy, and Darry head back to Adai, where living conditions are at least a little improved now that they have sunlight. The Black Siblings go hide out in the ruins of Bachika Village, and though they're more discreet now about fighting Beastmen, they still sometimes ride around to the various villages to report news. Yoko, Dayakka, Leeron, Tetsukan, and the other guys from Littner go back to Jeeha Village (since that's where their women and children are staying). And the rest of the Gurren-dan go back to their own respective villages, though Zorthy becomes restless because he hates his village, so he acts out and gets himself killed, and some of the other guys form gangs because they also can't really handle the idea of patiently waiting things out.
But Simon can't go back to Jeeha, or really any village in the area, because his face has basically been broadcast everywhere and since he's the leader, he's number one on the Beastmen's wanted list. So he goes traveling to find a far off village where no one knows him. Nia goes with him, because she's also really recognizable, has nowhere to go herself, and she just plain wants to be with him the most.
They eventually find such a village, where they enter the society as total strangers, and people are immediately suspicious of them. Simon earns some money by digging so they can at least get a small home to live in. For a while, Nia keeps herself hidden, wearing a hooded cloak when she's outside, because her hair and eyes make her stand out. But they eventually realize it's no use and she starts going around openly, maybe getting a job taking care of livestock or something.
Naturally, people are extremely curious about who they are, where they came from, why they're here, etc. These people still don't know there's a surface, so Simon and Nia are like aliens to them. And while Simon can at least fit in rather quickly since he's used to that kind of life, Nia is completely new to all this, which just adds to her alienness. Also, they start to really friggin miss sunlight and fresh air, and at times are only able to avoid sinking into depression by reminiscing about the surface together.
So several months go by. Simon and Nia are earning enough now to live somewhat comfortably (as comfortable as one can be in an underground village, anyway). And then suddenly Nia starts getting marriage requests from guys in the village. She's at a marrying age now and she's become popular among the young men because she's ~exotic~ and they want her as a trophy wife.
This freaks Simon out, especially once they start getting pushy because she keeps refusing. He gets worried that they're going to do something to her while he's not around, and sure enough, one day he comes home from work to find a group of guys surrounding her in front of their house, demanding that she choose somebody because a girl can't just not marry in this village! Some of them start getting rough, and Simon jumps in to protect her, which leads them to question who he is to her and why he should have any say in who she marries.
After firmly establishing that they are not related in any way, Simon is stuck coming up with an answer. Nia is still defiant, saying she doesn't want to marry any of them, no matter what they offer her. And now they're really getting angry, and the situation is starting to look dangerous, so Simon finally mans up and declares that they can't marry her because he's gonna marry her!
In the following silence, Nia looks pleased, and agrees to it. Grumbling, the men walk away, shooting glares at Simon, and Simon is shellshocked, because holy shit, he's suddenly engaged to Nia. That night, he apologizes to her for just blurting out something like that, but she reveals to him that she was hoping he would ask because he was the only one she wanted to marry. Daww.
So they get married. And they're already living together and stuff so it's not such a huge change, but they hadn't even kissed until the marriage ceremony, and then other young couples start popping out babies as soon as they're married and asking Simon & Nia when they're having theirs. This is all moving a little too quickly for Simon, and his anxiety shows, and Nia gets worried whether she inadvertently pressured him into marriage just because he wanted to protect her. And Simon isn't sure he even wants children, because he does plan on fighting again someday and what if something happens to him and Nia, and the kid ends up orphaned and alone like he once was?
Meanwhile, they make trips up to the surface every once in a while to check things out. Sometimes the Black Siblings would leave a note tied to a tree or something with news about the other members of the Gurren-dan (Nia would be the one to read it because Simon still isn't very literate).
That's all I've come up with so far, but I think the rest of the story will probably follow these three subplots:
1. Simon and Nia get used to married life and everything that goes with it, building their romance from the ground up.
2. The villagers start getting suspicious again because to them, Simon and Nia practically disappear off the face of the earth when they go on their trips to the surface, and soon they are living in paranoia.
3. Gradually the fight starts heating up again on the surface, led by the wild gangs formed by members of the Gurren-dan, eventually forcing Simon to get back into action before their chances of making a comeback are ruined once and for all.
So yeah, maybe once I've imagined the rest I'll post about this again, I dunno. >__>;