continuity issues

[Omenix]

In the opening sequence of the game Eon is shown to be human, yet after the events of SSA he becomes a ghostly flying head. This is how he appears in all the other games which means they occur after SSA. But, in a Kaos diary he says that his mother is in a mirror prison, the events of which caused this occurring in Swap Force, when Eon was a ghostly head. So how does Eon become human again? Also the hub itself is the Academy from Trap Team, showing it's set after the events of Trap Team.

I've only just unlocked the hub, so if there is some plot point after this that details why Eon is human, don't spoil it, I just thought this was interesting.

[Daphtaru]

I might botch this up some but I believe it's that Eon is still a ghost just not floating as a head in a machine.