It's definitely been at least 5 years since I read this story. It was long in length, over 100k words. I think that I read it on Fanfiction.net.
I've read so many that it's hard to keep things straight in my mind, but what I know for sure is that:
Harry Potter found one of the Peverell Brothers in an underwater tomb. In some sort of stasis I believe. I think that he put himself in a stasis to help the future generation find a way to defeat death. I think he realized that one of the brothers was alive because he couldn't use the Resurrection stone to speak with him. This may have been about 1/2 or 2/3 of the way through the story.
I can't remember if there was any pairing.
Harry's main goal was to find a way to defeat death, the motto on his family's tombstone may have been a motivation factor to him: "The last enemy to be overcome is death".
I'm pretty sure he did end up finding a way to finally defeat death, it may have also ended with space colonization, but I could be totally off on that part.
(This is not Significant Digits, though if you read HPMOR I highly recommend you read that.)