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Like the title says, Anakin choses the correct path and sides with Mace and the Jedi, however, he does not allow Mace to deliver the finishing blow to Palpatine and the Sith Lord escapes and still executes Order 66.

In this scenario...
Mace, Yoda, Obi-Wan and Anakin are all alive and kicking.
Padme, doesn't die and the twins are born into her care.
Palpatine remains in power, but has lost Anakin.
Most of the Jedi are still killed by the Clones, but there is no Darth Vader to finish the job.
The Republic is still reformed into the Empire and the Jedi are still officially traitors.
Because of Anakin's choice and Palpatine's escape, there is no final confrontation with Yoda and Palpatine.
The Separatist leaders are still in power and have control over their forces which are still under the overall control of Sidious, but they have ultimately outlived their usefulness to him.

How does the rest of the saga unfold?

I can think of two scenarios. However, in each of them the Separatist leaders are killed, they no longer serve any purpose with the droid armies deactivated and are promptly disposed of.

In the first scenario we see Yoda and/or Mace Windu along with Obi Wan training Anakin in secret until he is ready to take on Sidious.

In the second, and probably the more likely scenario, is going to resemble Episode's III's ending quite a bit, with the obvious subtraction of Kenobi going to duel Anakin on Mustafar. Instead Yoda, possibly one or more of those other Jedi might tag along with him, go to stop Sidious on Coruscant in a similar duel as the one fought in the OTL.

In either case if the Jedi manage to win quickly before the Empire begins to develop more they might be able to Salvage the Republic, otherwise Palpatine's death could create the same clusterfuck as there was after his death in RoTJ.

I see truce borne of necessity between the Jedi and the Separatists. Without the Jedi the Separatists are doomed and without the Separatists there is only exile for the Jedi. It might be a big pill to swallow for über patriots like Windu or Skywalker but neither are they the type to sit around and wait for the Rebel Alliance to get off the ground. With the Sith in firm control of the former Republic they may see the Separatists as the (much) lesser of two evils.

Darth Raptor wrote:I see truce borne of necessity between the Jedi and the Separatists. Without the Jedi the Separatists are doomed and without the Separatists there is only exile for the Jedi. It might be a big pill to swallow for über patriots like Windu or Skywalker but neither are they the type to sit around and wait for the Rebel Alliance to get off the ground. With the Sith in firm control of the former Republic they may see the Separatists as the (much) lesser of two evils.

Except that Sidious is still in cahoots with the Seperatist leadership, who are invulnerable on Mustafar and can shut down the vast majority of the Seperatist's armies with the (literal) touch of a button, and may do it. (Why should they believe the jedi and not Sidious? Heck, Sidious might have failsafes inside the bunker to active it, it's not that unreasonable).

EDIT: Put simply, militarily, the Seperatist's are a non-entity.
They might serve as a base to hide in, but anti-Jedi sentiment will be worse there than in the Republic, especially at such an early stage. (The jedi tying to them will make the PR situation even worse).

It's already a PR disaster for the Jedi. Throwing their lot in with the Separatists would simply confirm what everyone already believes. And the Wars are still going at this point, the CIS is down but not out. They've always doubted/mistrusted the Sith and when they're made aware that Sidious is the Emperor I doubt they're going to continue accepting his "suggestions". And if Sidious can shut them down from his office why bother sending Vader to do it?

The main danger here is whether they'll try to sell the Jedi out in exchange for whatever Faustian promises the Emperor makes. Even if they're forced into an asymmetrical guerrilla war like the Alliance in the early GCW all that stuff they have is hardly a "non-entity".

i'd expect the remaining Jedi to rally and launch an attack on Sidious himself, for without him there is no empire...

Windu already defeated Sidious. Yoda, Windu and Obi-Wan, teaming aganist Palpatine, would be pretty much it.

Darth Raptor wrote:It's already a PR disaster for the Jedi. Throwing their lot in with the Separatists would simply confirm what everyone already believes. And the Wars are still going at this point, the CIS is down but not out. They've always doubted/mistrusted the Sith and when they're made aware that Sidious is the Emperor I doubt they're going to continue accepting his "suggestions". And if Sidious can shut them down from his office why bother sending Vader to do it?

The main danger here is whether they'll try to sell the Jedi out in exchange for whatever Faustian promises the Emperor makes. Even if they're forced into an asymmetrical guerrilla war like the Alliance in the early GCW all that stuff they have is hardly a "non-entity".

With the death of Grievous the war is not likely to continue for much longer, there is no longer any need to keep the droid army going with the successful conversion from Republic to Empire and there is nothing stopping Sidious from doing what he did in the OTL (the only difference is that he won't send Anakin to do it)

The Sep Council is hiding out on Mustafar, where very few people (if anyone other than Sidious) know where they are.

Nothing in the OP is saying that the Rebel Alliance isn't going to form anyway, in all likelihood Bail Organa introduces them to the fledgling Rebellion in order to hide them. The Separatists fall but their war material and some of their people will eventually come over to their side that way.


addendum:

Regarding your question, "Why send Vader to do it?"

It wasn't just to shut down the droid armies, but also to make sure that the Separatists were all dead. Vader provided an easy way for the entire Separatist Council to end up as little more than strewn about body parts. Sidious had already compelled them into shutting down the droid armies before Vader had even arrived with the promise of a handsome reward. It would not have been to difficult to send someone else in Vader's place, although there were few beings, if any, that could succeed as well as Vader did.

Darth Fanboy wrote:Sidious had already compelled them into shutting down the droid armies before Vader had even arrived

This sounds a lot like a movie-vs-novel conflict.

NecronLord wrote:

Darth Fanboy wrote:Sidious had already compelled them into shutting down the droid armies before Vader had even arrived

This sounds a lot like a movie-vs-novel conflict.

Well admittedly I referenced the novel first, although what you've said raises an interesting point and I may have to pop in my RoTS DVD. Here's the scene from the novel for reference, Nute gunray is speaking with Sidious via holographic transmission.

RoTS Novelization p. 366 wrote:
"...Have your droid armies completed shutdown?"

"Yes my lord, nearly an hour ago."

Excellent! You will be handsomely rewarded. Has my new apprentice, Darth Vader, arrived?"

"His ship touched down only a moment ago."

EDIT:

And here is the part of the RoTS script, if there is something I am missing though corrections are appreciated.

RoTS Script wrote:

166 INT. MUSTAFAR-MAIN CONTROL CENTER-DAY

A HOLOGRAM of DARTH SIDIOUS is in the center of the room. NUTE GUNRAY and the REST OF THE SEPARATIST COALITION watch SIDIOUS.

NUTE GUNRAY: The plan has gone as you had promised, My Lord.

DARTH SIDIOUS: You have done well, Viceroy. When my new apprentice, Darth Vader, arrives, he will take care of you.

The hologram disappears.

I don't remember the movie as actually depicting the exact moment when the droid army is shut down, so I didn't think there was a conflict between the two.

Darth Fanboy wrote: I don't remember the movie as actually depicting the exact moment when the droid army is shut down, so I didn't think there was a conflict between the two.

When anakin calls palpatine and tells him that the separatists have been "taken care of," he tells him to send the shutdown signal to the ships of the trade federation.

Darksider wrote: When anakin calls palpatine and tells him that the separatists have been "taken care of," he tells him to send the shutdown signal to the ships of the trade federation.

Ah damn that's right.

If I remember correctly Mace and Yoda know that Sidious has been influencing the other side and almost exposed him earlier. Now they know Sidious is Palpatine and thus playing both sides.

I doubt Palpatine is going to be able to contain that little bombshell now. Especially as he went to all the trouble to play up Anakin and Obi as war heroes who will now be part of the group saying so. Plus if the Separtists remain viable, we could see mass defection and escalation if his loyalists don't back off and take Palps out.

I don't see Palps being able to hold it together after the tables get turned on him.

What bombshell? The Jedi Order (or what's left of it) has nothing in this scenario. No concrete evidence (who's going to believe the Jedi after they just tried to assassinate Palpatine?), no means of legal action, nothing.

A four on one confrontation, however, might be interesting. It's possible Palpatine may actually lose that

I'd love to know how he managed to escape in this scenario. Sith Smoke Bomb?

What if the Jedi Council had actually gone before the Senate after the death of Grievous had been confirmed and called for a vote to strip Palpatine of his war powers?

Darth Raptor wrote:I'd love to know how he managed to escape in this scenario. Sith Smoke Bomb?

I figure if Anakin stopped Mace's blow with his lightsaber instead of chopping off his hand, the two would at least have a little something to say to each other and Palps could just jump out the window or flee through his office.

There is no reason that he couldn't just blast them both with FL, but lets assume for this scenario that Anakin makes it very clear, very fast, that he is NOT going to side with Palpatine. Palpatine would certainly not want to go toe to toe with someone that just beat him AND the Chosen One.

Galvatron wrote:What if the Jedi Council had actually gone before the Senate after the death of Grievous had been confirmed and called for a vote to strip Palpatine of his war powers?

They would have most likely failed. The death of Grievous in no way means an immediate end to the Clone Wars, and the war is still raging. Furthermore, there's the matter of the reintegration of the Seperatist worlds (whenever they actually surrender or are defeated), the reconstruction of devastated regions, and the demilitarization of the Republic, all of which would require an executive with wide, overarching power.

Furthermore, not only is it highly dubious that the Senate could even strip Palpatine of his power (conversations in Ep. II and III heavily imply Palpatine holds his dictatorial powers until such time that he relinquishes it), but much of the Senate is either already in his pocket or decidedly pro-Palpatine (as evidenced by the nearly unanimous approval of Palpatine's rise to the imperial dignity and Mace's "He controls the Senate and the courts!").

TC Pilot wrote:What bombshell? The Jedi Order (or what's left of it) has nothing in this scenario. No concrete evidence (who's going to believe the Jedi after they just tried to assassinate Palpatine?), no means of legal action, nothing.

Like it'd take more then two seconds to neutralize that BS.

Joe Citizen: You tried to assassinate Palpatine.

Jedi: And if he's not a Sith Lord, how did we fail if we tried such a thing?

Joe Citizen: Uhm... uhm.

What's he going to do bring in corpses of the Jedi Masters with wounds from his lightsaber, and claim a magic sentient lightsaber defended him? Without Anakin his cover story is gone. As the novelization of the scene emphasized Sidious entire plan relied upon Anakin siding with him.

A functioning Seperatist movement means Palpatine can't consolidate power and put a blaster to the head of anyone that dares question him, while playing to various power parties. Yeah normal guy surviving a surprise assassination attempt by four Jedi Masters by himself is so, so plausible.

So how exactly is Palpy going to deal with:

Palpy: The Jedi tried to assassinate me, they're trying to take over.

Jedi: Palpatine is really Dark Lord of the Sith Darth Sidious who controlled the CIS and thus played both sides in an artificial war devestating planets, and killing untold numbers of people.

Paply: No I didn't.

Seperatist Leadership: Yes he did. It's all HIS fault!

Jedi: And if he isn't a Dark Lord of the Sith how would he have killed three Jedi Masters trying to apprehend him?

Even Padme revealed she had serious doubts about the state of the Republic, and the Revenge of Sith novelization indicates the Republic views the Separtists in general more as misguided then anything else. You have War Heroes and if I understand the novelizations preceding Revenge of the Sith a reasonable amount of evidence to tie Darth Sidious playing both sides, which Palpatine is not really able to deny he is, if he's playing the assassination card.

Palptaine should by all rights shortly face a Separatist movement engorged by states breaking away, and able to squish his now little Empire like a bug. The Republic side leadership would tend to take charge of the Separtist movement at that point given the unassertiveness of the Confederacies own leadership anyway, and in the process create a much more powerful Alliance to Restore the Republic at that point.

Imagine if Bail Organa had arrived early at the temple and convinced Mace Windu to accuse Palpatine of being a Sith Lord in front of the entire senate. Could the pro-Palpatine majority really resist the political pressure of the entire Jedi order and the Delegation of 2000?

FOG3 wrote:Joe Citizen: You tried to assassinate Palpatine.

Jedi: And if he's not a Sith Lord, how did we fail if we tried such a thing?

Joe Citizen: Uhm... uhm.

The rather blindingly obvious flaw in this argument is that this is exactly the same problem Palpatine faced in ROTS, which the novelization swiftly points out is that Palpatine's bodyguards intervened. You know, that whole legion of clone troopers that destroyed the Jedi Temple and wiped out about a thousand Jedi.

What's he going to do bring in corpses of the Jedi Masters with wounds from his lightsaber, and claim a magic sentient lightsaber defended him?

So only Jedi can use lightsabers? So only lightsabers can cause cauterized wounds? So "Joe Citizen" is going to know what a lightsaber wound looks like? So Palpatine is going to let the public see the Jedi Masters' corpses? So the Jedi are going to be able to present their argument?

The Jedi Order has nothing after Mace attempted to murder Palpatine. Their numbers are down to a handful, their public image is wrecked, their status is gone, and any ability they may have had to actually present their argument (they don't have one, since they attempted to assassinate beloved Chancellor Palpaitne on nothing but hearsay) just evaporated.

Without Anakin his cover story is gone.

Anakin was never part of any cover story.

As the novelization of the scene emphasized Sidious entire plan relied upon Anakin siding with him.

Of course it bloody well did. Without him Mace would have run him through. Palpatine's plan for the last several years relied on Anakin siding with him, or were you asleep while watching ROTS?

A functioning Seperatist movement means Palpatine can't consolidate power and put a blaster to the head of anyone that dares question him, while playing to various power parties.

Yeah. It's not like Palpatine controls the Separatists.

Yeah normal guy surviving a surprise assassination attempt by four Jedi Masters by himself is so, so plausible.

Yes, because the SUPREME CHANCELLOR of the Republic is going to be totally defenseless and exposed to assassination attempts. It's not like he has red guards or clone troopers to protect him.

*snip dialouge*

Except the galactic population hasn't watched ROTS. The Jedi aren't going to be able to present their case because they don't have one. They attempted to assassinate the head of state of the Republic, based on the flimsy excuse that their most emotionally unstable member thinks he's a Sith Lord, a member of a cult that was supposedly extinct a thousand years earlier.

Here's how the conversation is really going to go:

Palpatine: The Jedi attempted to kill me.

Jedi: Actually...

*clonetroopers draw their blasters and mow the Jedi down. The Senate bursts into applause*

Furthermore, why the hell would the Separatists out Palpatine? They don't even know he's Palpatine. Grievous wanted to disembowel Palpatine on the Invisible Hand, but Dooku stopped him.

Even Padme revealed she had serious doubts about the state of the Republic, and the Revenge of Sith novelization indicates the Republic views the Separtists in general more as misguided then anything else.

And what does that have anything to do with the Jedi's ability to out Palpatine as the mastermind behind the Clone Wars? Furthermore, Senator Amidala was in the obvious minority. Or did you not notice the "thunderous applause" of the Senate as Palpatine created the Galactic Empire?

You have War Heroes and if I understand the novelizations preceding Revenge of the Sith a reasonable amount of evidence to tie Darth Sidious playing both sides, which Palpatine is not really able to deny he is, if he's playing the assassination card.

What evidence? And even if there were, how can the Jedi possibly prove he's a Sith Lord? They can't force him to shoot lightning out of his fingers.

Think.

Palptaine should by all rights shortly face a Separatist movement engorged by states breaking away, and able to squish his now little Empire like a bug.

Or he can just play both sides off one another like he did for the last three years, or utterly destroy the Separatists on a whim, like, you know, he did in ROTS. Wiping out the CIS certainly is not reliant upon having Darth Vader to do it for him. Hell, Palpatine could do it on his own if he even deigned it worth his time.

The Republic side leadership would tend to take charge of the Separtist movement at that point given the unassertiveness of the Confederacies own leadership anyway, and in the process create a much more powerful Alliance to Restore the Republic at that point.

Sure, if any of the bullshit that conclusion is based upon were actually true...

TC Pilot wrote:What bombshell? The Jedi Order (or what's left of it) has nothing in this scenario. No concrete evidence (who's going to believe the Jedi after they just tried to assassinate Palpatine?), no means of legal action, nothing.

A four on one confrontation, however, might be interesting. It's possible Palpatine may actually lose that

The bombshell my Imperial Apologist friend is that Sidious is Palpatine. The only reason to have Anakin KILL off the Seperatist leaders was other then Anakin, they are now the only ones that know that they were working for a Darth Sidious. If they are ever captured and it comes out who they were working for...If that connection is ever made, then Old Palps will have the anger of millions of systems and their Senators come crashing down on his head.

One more thing, with out him having control of his office(assuming he can order 66 anywhere which is implied) How can he modify his office's security video to make it look like he was attacked by the Jedi meaning that the Jedi would have quick access to a film of what actually happened in the office.

How much more proof do they need anyway.

They have transcripts of a Sidious talking to the Separatists. They have tape showing a lightsaber wielding Palpatine attacking the Jedi. Since Palps has been calling the Separatists from his office they should be able to then get a location to track down them and get their testimony too.

The only reason to have Anakin KILL off the Seperatist leaders was other then Anakin, they are now the only ones that know that they were working for a Darth Sidious.

First off, the Separatists didn't know Sidious and Palpatine were the same person, only Dooku. They're not so mind-numbingly dense that they'll play along with such a farce if they knew that.

Secondly...

PALPATINE: "Their betrayal will be dealt with. After you have killed all the Jedi in the Temple, go to the Mustafar system. Wipe out Viceroy Gunray and the other Separatist leaders. Once more, the Sith will rule the galaxy, and we shall have peace."

ANAKIN: "Have faith, my love. Everything will soon be set right. The Chancellor has given me a very important mission. The Separatists have gathered in the Mustafar system. I'm going there to end this war."

DARTH SlDIOUS: Now, Lord Vader, now go and bring peace to the Empire."

If they are ever captured and it comes out who they were working for...

Captured by who? The Empire?

They don't have to know that Sidious = Palpatine idiot.


They just have to testify that they are working for a Darth Sidious.

And captured by the Jedi stupid.