Chapter two has the players investigating who the Sinister Traitor is, trying to find out who dropped a dime on them - eventually gathering enough evidence to convict Var Narek. That's all well and good, but the chapter ends with something like "After the players have gathered enough evidence, they go to the commander. . . "

Egads - what an optimistic author! The players presenting their evidence and NOT arresting/capturing/shooting on stun until unconscious Narek first? And seeing that Chapter Three kind of depends on Narek getting away, one might have included a provision of "So your players go and shoot Narek".

Oh, to be free and unencumbered of completely paranoid players, as to allow Narek to get away unopposed like that. . . .

I haven't read the adventure, but isn't this easily solved by just saying "if your players go to shoot Narek, then they find their investigations have tipped him off and he's already fled"?

Agree it probably should have been addressed by the author(s) though - it is a pretty common PC reaction!

Even better, let them stop him only to find out they have to chase down his partner (that you made up on the spot if need be) in the next act.

I haven't read this adventure either but have you thought about revealing Narek is just the cats paw and someone else is the traitor?

Better yet have them deliver Narek and then reveal he's been broken out by a confederate or even killed whilst in custody as the conference with the commander reveals a plot hole (there's usually one no matter how well written an adventure is after all!).

What if Narek had swapped places with someone and the person whose been posing as him is the one the PCs caught but noone figures that out until they discover Narek's codes are still being used even though he's locked up and when the PCs go to check they discover he's been killed...

Exactly who knows who Narek is?

And what if you're dealing with a member of the shapeshifting race like the female assassin from Attack of the Clones?

Would be a handy way to be in two places at once let alone have an alibi in case they're found out...

And what if the shapeshifter is the one killed?

Well there's proof Narek couldn't have been the one...

What if Narek had swapped places with someone and the person whose been posing as him is the one the PCs caught but noone figures that out until they discover Narek's codes are still being used even though he's locked up and when the PCs go to check they discover he's been killed...

That's a little unfair on the players. If they've figured it out changing reality on them is harsh, imo. This is one reason I don't run modules very often - I like a sandbox-y approach and it's way too easy to end up in a trap where you have to either railroad the players like this or abandon the module. :/

I've not read the adventure. What happens if he doesn't get away? Is everything ruined or could the game carry on in a different direction?

I so hate body swappers, and shapeshifters being used as a plot device. it is cheap and poor writing.

much prefer the catspaw

I agree with the rest that the swap isn't a good option.

I would go with either an accomplice releasing him after the characters capture him, or that that he was working for another traitor – and he reveals this to the players once captured – who has split when Narek was taken down.