Storyline scenario between WWE Draft and WrestleMania 33:
Early on, Shane and Stephanie runs both Raw and SmackDown. Then, Triple H returns and ambushes Shane. Steph of course would side with Triple H. This leads to Triple H vs Shane where "Loser Leaves Raw". Triple H wins, which leads to The Authority running Raw while Shane runs SmackDown exclusively.
Fast forward months later, The Rock returns to Raw as a "free agent". He would appear on both shows for a week. Following week on Raw, Rock must make a decision to either appear on Raw or SmackDown. The Authority makes an insult towards The Rock, which leads to him signing with SmackDown on a "short term deal".
Rock would appear on SmackDown exclusively, but not every week. On an interbrand PPV, Triple H (or one of the members of The Authority) costs The Rock a match. This leads to Rock "invading" Raw and requesting a match against Triple H at WrestleMania. Triple H accepts the challenge.
Shane would add the stipulation that if Rock wins, The Authority is no longer in power. The Authority counters by saying if Triple H wins, Rock can no longer appear in WWE again. At WrestleMania, The Rock def. Triple H. The Authority are out of power for good. No clauses, no BS. G-O-N-E. This leads to Shane appearing on both shows, but instead appoints new COO's for both brands. Rock would become a free agent after WrestleMania and returns to films.