The Fifth Edition core rulebook has a section on alternate campaigns in the GM chapter (SR5 p.350-351).
The original Shadowrun Companion sourcebook (both SR2 and SR3 editions) had a section on alternate campaigns, including DocWagon ("Where Does It Hurt?" p.109), news media ("Smile, You're On Camera," p.113), special forces ("Trained to Be Ghosts," p.114), law enforcement ("I Am the Law," p.116), magicians ("Double, Double, Toil and Trouble," p.119), and gangs ("This Is Our Turf, Meat," p.120).
The SR2 Missions sourcebook also explored alternate campaigns, including Lone Star ("Under the Influence," p.5), DocWagon ("Malpractice," p.26), Ares corporate security ("Mission: Mars," p.52), or UCAS special forces ("King of the Mountain," p.73).