This is for those who have not read "Jedi Harris" or "Terran Jedi"
In 1997 on Halloween, Ethan Rayne cast a spell turning all people who bought costumes from his store into their costumes. For a few hours, Xander Harris in the "Jedi Harris" time-line, was Obi-wan Kenobi.
In 1998, Cordelia Chase made a rash wish unwittingly to a Vengeance Demon, Anyanka. The wish was for Buffy Summers to have never come to Sunnydale. What followed was Xander Harris instead wore the costume of Darth Vader. Matching his anger and hateful mood as the year before, the Master escaped his prison during the events of the Harvest and slew his best friend, Jesse.
After the Halloween incident, he retained the abilities of a Sith (Darth Mortalis). Willow Rosenburg discovered this truth and was killed by Xander. Soon after he is recruited by Mayor Wilkins. Xander discovers Wilkins' plans for ascension and kills him. He becomes Deputy Mayor and eventually Mayor of Sunnydale. Xander uses his skills and position to defeat the Master (nailing his skeleton to a tree in front of the high school as a warning). He also exterminates most of the demons in Sunnydale. When the government starts looking into setting up the Initiative, he offers his knowledge of advanced technology and ends up working with Professor Walsh at the facility. Eventually, he becomes head of the facility.
In the original time-line, Colonel Harry Maybourne comes to the Initiative to investigate and opposes Harris, he is imprisoned. Harry anticipated the possibility and sent word to Jack O'Neil of SG-1. SG-1 came to Sunnydale in search of Maybourne. They became involved instead with Rupert Giles and the White Hats who fought against Harris with the knowledge that he was a Sith. The Riley, Graham, and Forrest rescue Maybourne and join Giles' group.
A combined SG-1 and White Hat attack successfully slew Xander and destroyed most of the Initiative. Meanwhile, Cordelia revealed all she knew of the previous time-line and Giles managed to summon the Vengeance Demon, Anyanka, to force her to reverse the wish. He succeeded in destroying her amulet which reversed the wish, restoring history as they knew it with Xander being a Jedi instead of a Sith.
This tale explores one possibility with slight changes on what could have happened if Xander, the Sith had not been defeated but lived on to continue his plans.