We all know Ahsoka is never mentioned by anyone in Revenge of The Sith, so she must still be Anakin's Padawan just merely sent on a solo mission that doesn't arouse any suspicion or worry among the cast of Episode III. Besides, Anakin and Obi had bigger fish to fry on Coruscant that would have taken a lot of their focus.
If Ahsoka was still Anakin's Padawan this helps support the fact that the Jedi Council refuse to give Anakin the rank of Master in Revenge of the Sith because he is still training Ahsoka. A Jedi is granted the rank of Master AFTER they have trained their first Padawan.
Ahsoka's mission would be to hunt for Asajj Ventress who disappeared after the Battle of Boz Pity as detailed in the Star Wars: Obsession 4 and 5 comic.
This scenario is an attempt to bridge existing SWEU with TCW continuity. Read up on this Wookieepedia article before continuing unless you have already read the Obsessions series and in that case, you may proceed.
Here's the lowdown of my scenario:
1-Ahsoka goes on a solo mission prior to ROTS to hunt Asajj
2-Goes to Unknown Regions with Alpha and Rex
3-Finds Asajj, makes peace with her after nearly falling to the dark side
4-Order 66: Alpha goes to kill Ahsoka, Rex stops him
5-Ahsoka and Rex return to Coruscant
6-Seek out any surviving Jedi. Ahsoka wants to kill Vader without knowing he is Anakin.
7-Joins forces with Olee Starstone and Chewbacca
8-She along with a few other Jedi start a war against Vader
9-The Force leads her to Tatooine where Obi-Wan tells her to stop chasing Vader and go into hiding. She refuses. Says farewell to Obi
10-In the Confrontation with Vader, she discovers he is really Anakin.
Nearly all the Jedi she is with are defeated. She is struck down by Vader
The Outer Rim Sieges
Just prior to ROTS, Alpha-77 (one of the original ARC troopers who fought with Anakin and Obi in the comics) would have managed to find his way to civilized space after Asajj dumped him off on a barren world in the Unknown Regions and killed the rest of the crew of the Republic Medical Shuttle she had escaped on. Alpha would report to Republic Intelligence that Asajj still lives and Ahsoka would be sent by the Council to lead a mission to hunt Asajj Ventress as her first solo mission.
She, along with Alpha, Captain Rex and a small contingent of clones from Torrent Company would head to the Unknown Regions where they would find and confront Asajj.
Asajj at this point would only want to be left alone because Dooku betrayed her. Ahsoka's recklessness and anger at Asajj would overcome her and she would nearly kill Asajj in a rage before Asajj defeats Ahsoka and convinces her she no longer follows the Dark Side or the Separatists and just wants to be left alone.
At this point, the Clones would be given the command to execute Order 66 and Rex would refuse the Order while Alpha would want to go through with it. Rex and Alpha argue and Alpha goes to shoot Ahsoka while she is distracted but Rex tackles him and Ventress saves Ahsoka by deflecting the shot. She goes to kill Alpha only to be stopped by Ahsoka and Rex who tie Alpha up.
Rex and Alpha explain to Ahsoka about how the Jedi have now been branded traitors, Rex explains why he refuses to kill Ahsoka and Alpha calls him a traitor. Ahsoka wants to return to Coruscant to see if any Jedi survived even after Rex's pleads for her to go into hiding but she refuses and prepares to return.
After making peace with Asajj, who is now neither light or dark, Rex reluctantly agrees to accompany Ahsoka to Coruscant after ditching his clone armour. They drop Alpha off at a Spaceport on the edge of Known Space and continue to Coruscant.
On Coruscant, she would see the destruction of the temple and would be confronted by troops from the 501st who hesitate when they see Rex and Ahsoka (their former commanders) but open fire on them forcing them to retreat.
Alpha would return to Coruscant where he reports to Vader that Asajj and Ahsoka still live and Vader would be overwhelmed by emotion because this brings back painful memories of the time he was Anakin Skywalker. Memories he wanted to forget. Ahsoka would learn that Vader murdered everyone in the Temple and would seek him out directly without knowing he is really Anakin Skywalker.
Vader would be confronted by Ahsoka but would refuse to fight her. She falls deep to the Dark Side as she becomes overwhelmed with grief and nearly kills Darth Vader before realizing he is not fighting back and flees once she discovers he was Anakin.
She would find several Jedi survivors and along with Rex would lead a rebellion against Palpatine. She would join the crew of the Drunk Dancer, alongside Chewbacca, Olee Starstone, Lu Poorf, and Nalual, who all vowed to fight the Empire in any subtle way they could at the end of the novel "Dark Lord: The Rise of Darth Vader" and become a leader in the "Pre-Rebellion." Ahsoka would lead strikes against Imperial targets and discover and protect more Jedi who would join the crew aboard the Drunk Dancer.
Vader would eventually overcome his emotions and wish to destroy everything about his past including his padawan. However, his first target of his past would be Asajj. Vader would hire bounty hunters and send Stormtrooper elite to find Asajj in an obsessive hunt. When he discovers that she is hiding in the Unknown Regions, he travels there to confront her.
Meanwhile, Ahsoka's travels would take her to Tatooine where she would meet Obi-Wan. Oi-Wan confirms that Anakin is indeed Darth Vader and there is no longer any hope for him to return to the light, but Ahsoka does not believe that. She refuses Obi-Wan's advice to disappear and not confront Vader and say her farewells.
When Ahsoka learns that Vader is travelling to the Unknown Regions, she leaves with a Jedi strike force to confront him and bring him back to the light.
Ahsoka and Asajj join forces to fight Vader. Asajj would be defeated by Vader, and the Jedi Ahsoka came with would slowly be struck down by Stormtroopers as well as Vader's blade.
After a long duel between Ahsoka and Vader and she knows she is beaten, through the Force she shows Vader everything he has lost, his wife, his kids, his life, and asks him if it was worth it. Vader feels remorse, and for the slightest of seconds he is Anakin again. However that emotion was short lived and Vader's anger quickly took over. Ahsoka lets herself get cut down by his blade knowing that there was still good in him.
Rex and the crew of the Drunk Dancer would continue to fight the Empire and eventually join with the Rebellion. After a few years Rex would decide to settle down with a wife on a secluded Outer Rim world away from the fighting...