Watched the key openning/closing vids again.  Couple of things are clear:

1 - the ship at the beginning taking away the ISA nuke is a Helghast ship.  Their is no ISA ship involved.  The ISA logo is on the nuke only and the ship is clearly Helghan.  It leaves as Visari enters the building to make his address to deliver the nuke exploded in KZ2.

2 - Visari therefore doesn't leave on the ship or their is no evidence he does.  It's taking the nuke and the guard is killed presumerably to keep the source of the nuke hidden.  Radec and Stahl of course know about it but it's unclear who else - Orloc, his daughter, the other generals or whatever they were?

3 - The above strongly implies that it was to be kept secret Visari muked the city (otherwise no need to shoot the guard).  This plot strand seems obvious but hasn't been covered further yet or is just plain muddled.  In fact the whole nuke plot doesn't seem to make sense given the closing moments of KZ2 and openning sections of KZ3

4 - Orloc is dead I'm sure given Stahl kills him in plain sight so I think we can leave him out of any thoughts on the ending.

5 - We see Visari killed in KZ2 but clearly they could pull a switch.  The daughter thing is a poor hint though I agree.  Maybe she just feels uncomfortable about the nuke stunt - assuming she knows, which isn't made clear - or maybe he is a double... again, this plot strand isn't too clear as of yet.  But hey, it worked for Castro in COD:BO so who knows

6 - We see Stahl run like hell when he realized the nuke's inbound to his ship.  Clearly he's abandoning his plan and running somewhere with purpose.  In classic bad guy termination if he knew he was doomed he'd have stood still and taken it.  Ye he runs.  We see the ship explode but we don't know he's killed or not.  He might have got away in an escape pod

7 - there is the poorly explained stuff about Visari being in negotiations and some sort of cease fire being arranged, with Stahl meanwhile going rouge with his plan to decimate the Earth.  It's really not clear - due to poor narrative TBH - who's involved in which plot and why - i.e. what do they expect to get out of it.

8 - In the closing scene the device could either be an escape pod or a bunker.  The framing doesn't make it clear.  The shadow is also hard to make out.  Could be bald head - Visari? - but hard to tell.

So... on the evidence you have to assume - unless they're introducing yet another new face - that it's either Stahl from an escape pod or Visari and there was a double.

I've got to say, thinking about it the whole thing is muddled.  I think GG have been making it up a bit and the plot across both games is now looking flaky.  Take the nuke the city thing.  It was presented in KZ2 as a desperate last resort, rather than let the city be taken.  Then at the end of KZ2 - and now confirmed in KZ3 - massive re-enforcements arrive and the ISA are way outgunned and outnumbered.  So why the nuke?  Visari would have known they were about to spring a huge counter attack.  In fact why was did he leave himself exposed when - as shown in KZ3 - all the other senior guys managed to keep themselves safe.  The only reason to nuke would be a secret plot to blame the ISA and create more hated.  The shooting of the Helghan troop and air of secrecy at the start of KZ3 would seem to confirm this, but it's just terribly unclear.

Nah.  GG are making it up and already across the two games I've played there now seems to be lots of contradictions.  The plot in each gives enough impetus to the action but is pretty woolly as a while I think.

The ending cutsceneI think is pure - dum dum DUM - stuff with no logic to what went before.  Heck, we get told there is silence from the planet - literally no one alive - then the next minute we've got troopers sauntering around unaffected by anything and rescuing someone from an escape pod or bunker?  Where did they come from?  Is the planet still silent?

Maybe things will come clear going forward, but for now I'm going to enjoy the game for what it is and not worry about the plot anymore.

In kz2 I thought they nuked their own city to wipe out all ISA forces present there. Though the petrusite Tesla coil shield thing was said to have decimated the ISA forces already. In addition it seems Narville and some other troops had evacuated after the petrusite shield event as Sev meets them outside the city after the underground petrusite grid was blown up.

Off course the nuke was used as propaganda against the ISA as well. And in the opening of kz3 Stahl and Radec shoot one of their own soldiers as the ship takes off with the nuke to silence him.