The main idea behind Sea Dweller Lowblood is that the Sectarian Revolt alluded to in Mindfang's smut journal was successful, and the hemospectrum was effectively reversed. Karkat's still
outside the normal color range, but now he's is close to the Empress rather than the lowest of the lowblooded peasants. Also, Cancestor is considered a national hero rather than a dangerous revolutionary who was erased from history, and there's this religion who worships him and sees Karkat as his reincarnation. His blood is as mutant as ever, but now it's mutant in a
good way.
Oh, and spoiler warning, I guess.
Since Homestuck is still in "nothing is happening"-mode, I might as well advertise some other fan adventures I've enjoyed.
Prequel is about an alcoholic Khajiit traveling to Cyrodiil to begin her life anew, get a real job, stay out of jail, and not get into any more trouble with cults. It goes about as well as you'd expect. The author, Kazerad, has something of a record for tormenting catgirls. Knowledge of TES: Oblivion is not required to enjoy the adventure, although it probably helps.
Waterworks is less sad and introspective and more adventure-y. A woman sneaks into a local water pumping station to find out why the water has been out for the past week or so. Quickly turns into an epic quest to defeat the squad of water-themed thugs and rescue all the plant workers. Later turns into an epic quest about the fate of the universe or something. Honestly, I don't even know what is going on any more.