Here are some ideas for you're stories to get started - 

  • Pick up at Season 2, but make it an alternate Season 2 and have it to where Jesse indeed did die in the season 1 finale, have one of his friends be Walt's new partner, or have Walt search for a partner and find someone else. 
  • Have it to where they failed to kill Gus and he "owns" them. 
  • Have a version where Gus or Victor never died, and they later come in handy, but if you choose Gus not dying, their may be some serious consenquinces for Walt. 
  • Have a version where Hugo never got arrested and is making trouble in the school, maybe Walt has to kill him with sciene powers. 
  • Have a version where Ted gets Skyler pregnaut and Walt has to "Take care" of it. 
  • Have a version where Mike doesn't get killed. 

Anything you want, feel free to add ideas!