It's not broken per se but i thing a few tweaks could make this arc a little more fulfilling.
Most important thing would be to let O`Brien escape instead of exploding with the ISS Molly in Bajor system.
The whole point of the shuttles rigged to destroy the wormhole is to provide a diversion and give him time to ecape.
Slipped though our grasp we should meet him again on the other side of the mirror after we crossed over to retrieve the orb.
That mission is supposed to be the conclusion of the arc but has nothing going for it.
It was foreshadowed heavily by the prophets and The Sisko as our great destiny and makes us expect something a lttle more epic.
Use O'Brien as the Big Bad and give him an endgame that we need to prevent.
For example make him use the orb to become something equal powerful like Dukat in DS9s finally that threatens both universes.
Make us fight O'Brien on the ground in the cave and retrieve the orb, but not before he completes his ascension ritual.
We beam up and find him in space as this nearly god like being that can only be destroyed by the combined power of our ship and a small fleet of Commander Shelly who is letting us leave but threatens to return of course.
And I realize ithis will make the fire cave story a little redundant but could be used more effectively here.
Where did I say he should be the Empire`s leader?
Just the mastermind behind the Orb plot...
He has already been established as such at the end of Tear of the Prophets.
So all they need to do is show us the consequences of his endgame for an emotional pay-off and something that lives up to the phrophecy from the wormhole aliens.
But it`s kind of silly that the big boss of the plot dies one chapter before the big climax and leaves only his nameless red shirts to fight us.
I would really like to see what the whole point of his plan was.
Regarding the Emperor/Empress leave him/her for a future story, like a new weekly series. Pratically writes itself
Of course it has to be a shocking revelation of his/her identity as someone we already know.
Most logical candidate in my opinion would be Sulu.
Joking aside, I felt the O'Brian arc was rather forced. I do believe the mission text points to him being the "leader" of the Empire, having killed his father in order to lead the Empire. The entire plot was just... meh. Felt like filler. I also thought the "destiny" spoken of was simply returning the orb, though you might extend the later Q mission as part of that (saving Sisko and all).
By the way... has anybody ever had that slight bug where O`Brien was standing outside of the forcefield when you reach the guy?
Was lauging my ass off when that happened because i was haveing a whole conversation with him during which I could have always put handcuffs on him, let him tackle by my security team or just beam him into my brig before he made his daring escape via transporter.