After reading Triple Zero, there are a lot of new developments one can consider ~ Etain and Darman for one, Kal's quest for vengeance, &c...

People speculate all the time, but Karen Traviss has hinted:
I won't say any more about Order 66. Better not. But nobody's close.

The main point that comes to mind is Order 66, and how Omega would handle it. Either they kill Etain or they don't. Right?

No.

Karen has said multiple times:
All I'm saying is that people tend to take a bipolar view of the possible outcomes of Order 66 - either "Darman kills Etain" or "Darman refuses to kill Etain".

But I can't even begin to count the number of possible storylines beyond that.

There are a lot more options to consider from all different standpoints.

Take Omega Squad for instance. We've already seen that Republic Commandos seem to have formed their own personalities even among their squadmates. Just in Omega Squad we have Niner, who is the consummate soldier, Fi, who considers his orders with his conscience before he acts, Darman, who we already know cares for Etain but still thinks of himself as a soldier, and Atin, who is a wild card in the fact that he's the member we really don't interact with a whole lot.

Given their different personalities, it's feasible that when Order 66 comes about they're split down squad lines.

Also, the way the operate has to be taken into consideration. They are pretty much self-reliant. They get their orders, get inserted, and don't come back until their job's done. As the Jedi get spread so thin, it's even possible there's no Jedi around. Heck, how do we know they even get the Order? For all we know they're off on some Force-forsaken planet with no communications of any kind.

Yet another point to take into consideration is the Clones lifespans. Not only do they age faster than regular men, but they don't exactly take on jobs conducive to long-life anyway. And there is still about a year and a half left of fighting before the Clone Wars end. It's not the most appealing of theories, but could it be they (or at least Darman) is killed before Order 66 is even given.

o:o:o

Let's consider Etain for just a moment. Like I said, there's still a year and a half left in the war. That's plenty of time to have a baby, especially when she says she can speed things up to only a few months.

First thing that comes to mind would be the Jedi Order's reaction to this. Taking a guess, I'd say they wouldn't be too happy. It could be that they overlook that small issue in favor of their still needing Generals, but it's also possible that she's not even a part of the Jedi Order anymore. Meaning she's not a General when Order 66 is given and is no where near the front lines.

If she is still a General. It's a big galaxy, and the chances of her being with Omega Squad at the time are probably nill. It's still something to consider, but as a General, she normally wouldn't be running around with Special Forces on their missions.

Even if she's a General, the Jedi are dropping left and right. Like Omega, it's a war, what if she's been killed already? There are plenty of ways to kill a Jedi without meaning to, especially during battle.

And while we're thinking about her, let's not forget this kid of hers. Has anyone considered the implications of a Force-sensitive Mandalorian running around?

These are a formidable people anyway, what's going to happen if one of them can manipulate the Force? There's also the whole concept of possible falling to the dark side seeing as he isn't trained, and a whole host of other problems a Force-sensitive will face. We haven't forgotten Vader and his purge of Jedi have we? It's wholly possible that this kid gets swept up in Vader's hunt. Or even that he's scooped up by the Emperor to become a Hand.

o:o:o

And what about Kal's vision for the future? We can't forget that he's got the Nulls searching for Ko Sai in hopes of giving them all a full lifespan.

What if he finds her and she is able to give them that life?

Kal's whole plan is to take the Nulls, Omega, and any other clones he can get his hands on back to Mandalore and have them lead "normal" lives. If that happens, will they still obey Order 66? And if so, will they do it, or will they have lost the whole concept of taking orders from the Republic?

But there's also the chance that that didn't happen by the time the war ends. As the Emperor-to-be tells Anakin: "Our Clone Intelligence units have located General Grevious." And it's possible he's referring to Kom'rk and Jaing or another of the Null ARCs.

Continuing on that vein leads to more questions regarding the Nulls. Is he referring to the Nulls or are there other intelligence units out there? Of course it's possible that there are; seeing as everyone seems to acknowledge the Nulls as Kal's private army.

But given it's the Emperor saying this, and (as Darth Sideous), he already knows Grevious is on Utapau, he could be making the whole thing up - and most likely, he is. For all we know, the Nulls have disappeared completely and there are no Clone Intelligence units at all.

o:o:o

It's all circular thinking in a sense. We're considering "what about Order 66?" when there are still the events of a year to consider before Order 66 even takes place.

Thankfully, we can infer a lot by Karen's comment that she has their lives planned out:
from birth to Order 66 and beyond.

That phrase in and of itself could be a clue as to their fates, but it leads to another round of questions. Foremost being: Who is "they"? Omega and the Nulls? Who else with them?

Either we'll learn more from the upcoming "A Practical Man" and "Bloodlines" or we have to pray "Triple Zero" sold enough to warrant continuing their adventures in another Republic Commando book...