Top of Crystal Tower [Spoiler discussion.... maybe]

[EdwinLi]

well since the crystal tower is supposed to be emulating the original crystal tower I would assume at the top is the cloud of darkness or perhaps perhaps some allagan thing that fuses with that garlean dude to act as a cloud of darkness

and hopefully we also get to go to eureka and fight scylla too underneath the tower

Well we know that each Humanoid boss we will face will be the final boss of each floor and they will be from FF3 but each will have different lores to fit into FF14 since each one are the Original Heroes of the Alagan Civilization.

For now I can only guess we will fight Xande as the first stage of the final boss and once we defeat him, just like in FF3, Cloud of Darkness will appear.

Once the final boss in CT is over a cutscene will probably play when we leave the dungeon to conclude the CT storyline and surprise we see Omega weapon inactive on the top and "That Garlean" on Omega Weapons Shoulders. Then we have the obvious evil antagonist Monologuing then say the classic "I would kill you now but I'll wait to do that later" speech and finally he activates Omega Weapon and leaves Crystal Tower with it to foreshadow Omega Weapon as the Final Boss for a Future Main Scenario Story.

SE will probably do this so CT can serve to explain how "That Garlean" got his hands on Omega weapon once we see Omega Weapon in Ishgard storyline (the first expansion) or Garlean Empire storyline (unconfirmed if Expansion or Major update).

[BoomerOU]

Since SE said they are tieing CT in to FFXIV by turning Xande into an ancient Allagan Emperor named Xandes, I can see him inside trying to resurrect an ancient piece of machinery, possibly Omega Weapon.