Read threw this carefully.
Some time or another (Piror to FF6) Sabin will (Supposedly) be chosen to be his master Duncan’s successor.
Sabin will be told that Vargas (Duncan’s son) will be the successor – which would make more sense. However Vargas him self will be told differently, and believe it is Sabin who is “The chosen one”.
Vargas becomes angry as he though he was going to be the successor, and feels unwanted by his father.
This much is stated in the game.
After this the game states that Duncan is dead (Murdered by Vargas) only for him to return much later in the game.
Where has he been?
Think of this.
The returners led by Bannon will appear more frequently after Duncan’s “Death”.
Bannon is now more involved in his own army.
The returners know (through Bannon) that Sabin is the person they might need for the fight against the empire.
Locke and Edgar (The later is related to Sabin) are instructed to take Terra (Someone else the returners need) to the returners Hide out. But the way they pass a house. (I shall come to this later)
Vargas arranges to meet up with Sabin on MT Koltz to settle there differences. (Sabin Knows about Duncan’s “Death”).
At the house a man conveniently tells Locke’s team that Sabin will possibly be at Mt Koltz. Although he has no apparent reason too.
The team will find Vargas and will be defeated and then Sabin arrives.
Once Sabin has shown his strength Vargas escapes never to be seen again.
Sabin Joins the Returners as was planned all along by Vargas and Duncan.
After Kefka damages the world, All the official Returners except for Locke, Edgar, Sabin and Bannon will die.
The war between Bannon and Geshtahl is over and both Armies are almost completely destroyed.
There is no need for Bannon (Who doesn’t really exist) to be around anymore. So he vanishes giving the impression he died with the others.
Duncan now reveals he’s alive now that Bannon is “Dead”.
Do you see the conspiracy?