Color coded for everyone's convenience
-Terranort comes back to life (Heartless then Nobody died).
-Sora & Co. search the worlds for the people "still suffering" as Jimminy's Journal put it.
-Aqua gains resolve to find the Door to Light (from her conversation with Ansem the Wise).
-Terranort's heart is still fighting for power between the two that compose it, and every so often, Master Xehanort gains power and Terranort corrupts more and more people.
-The corruption gets noticed by Sora & Co. and they try to fix it.
-The corruption effects the Realm of Darkness, too. Aqua sees this and she tries to fix it on the Darkness side (I see the corruption being the Unversed, which she would recognize, but Sora & Co. would just see as new enemies).
-Terranort begins to fall back to the Darkness (both Terra and Master Xehanort, that is).
-Sora & Co. seal off worlds in an attempt to stop the corruption.
-Aqua must unseal the worlds to leave their borers (unknowingly undoing Sora's work). She believes the corruption has made the worlds' hearts loose sight of their (potential) allies.
-King Mickey tells Riku to go and reseal the worlds in the Realm of Light, and the King goes to the Realm of Darkness in an attempt to find out what is making the worlds seemingly unseal on their own.
-Riku reseals the worlds as the corruption spreads like wild fire.
-Terranort falls on the precipice of Darkness.
-Aqua fights Master Xehanort (next to a comatose Terra) in the Realm of Darkness.
-At the behest of Ansem the Wise (who is connected to Riku's heart after the events of Days and KH2), Riku fights Terranort in the Realm of Light in an attempt to stall him from causing an irreversible imbalance to the worlds.
-Terranort falls to Riku as Sora shows up on the scene. From his weakened state, he can no longer remain as "Terranort", and he splits into Terra and Master Xehanort (with Terra in a coma from the lack of a complete soul).
-Sora fights Master Terranort.
-King Mickey finds Aqua in the Realm of Darkness and they begin to leave the Realm of Darkness.
Aqua is a popular character, and Nomura already said that the multiple scenario games (at least, for KH) were better (to play, to create, I don't remember).
The characters that would be played (I think) would be Aqua, Sora, and Riku.