I wrote three stories, actually. The first one is right after X8. Sigma and Lumine do come back, but so do Sting Chameleon and Magma Centipede. The latter two are good now, and cured of the Maverick virus. This is mainly due to a third character. The three of them team up with X, Zero, and Axl, and destroy the Mavericks for good.
The next story deals with the aftermath of the Maverick Wars, and a young human villain who had close ties as a kid to X, Sting, and several other of the Reploids who turn Maverick. In a twist of fate, X temporarily turns Maverick due to the actions of this human, and his friends are forced to battle and save him.
The third storyline is much larger, and incorporates sci-fi elements that have not been used in the Mega Man Universe yet. It explains the origins of the Maverick Virus cure (the cure was not created by either humans or Reploids), and how Sting and Magma came back. It also features a powerful, destructive force far greater than the Mavericks.