Before you face the E4, N will show up and want to summon both legends with his Orbs. Geechisu shows up and stops him from using both the Black and White orbs. Geechisu somehow manages to combine them. Since that has happened Yin (Reshiram) and Yang (Reshiram) start fighting . There is an epic cutscene when they are fighting.
(this is not how I envision the cutscene. it should be in 3D)
Meanwhile the gym leaders fight the sages. Apparently you have to go find Kyurem to stop the madness. When you find Kyurem (location moved to Victory Road) you realise that it does not want to help you at all until you are proven worthy. So you go to fight N and when you defeat him in which he reveals that Geechisu has tricking him. So you go fight Geechisu with his BW party and he gives you his Grey Orb.
So you go back to Kyurem and it challenges you to a battle. When you catch it and bring it over to Reshiram and Zekrom they will stop fighting. But then Geechisu intercepts with his Tao Necklace (used to control the Reshiram and Zekrom) and challenges you. When you defeat Geechisu once again he and the sages leave. Both of the legends flee back to the Dragon Spiral Tower (They are to be challenged after beating Iris later.)
N realizes how much of a fool he was; for joining Team Plasma, for trying to free Trainer's Pokemon, for all the other things he had done. So he goes to the Grey Ruins/Castle where you can rematch him after you beat Iris.
You fight the Elite 4
AND the champion this time. You do the usual and new aftergame stuff. (Like battling Iris, capturing Reshiram and Zekrom.)
Note: I tried so hard to not make this an emerald clone.
ROM hackers feel free to make this.