I read this story a while back. It takes place in Season 6. It's not too long a story, I think it only had like 3 or 4 chapters. Spike and Buffy are having a heated argument, I think before As You Were, which results in Spike saying something like «that's just it» about a comment Buffy made about him being soulless. He then takes off to Africa to get his soul back, meanwhile everything else in Sunnydale is happening, just without the whole Seeing Red bit, like Willow trying to blow up the world and such. That's all I can remember other than it was in the dark-solace site where I read it.

I managed to find it myself finally. It's Dissonance by Twinkles. It also seems like I was remembering some things incorrectly.