The Clone Wars Era in the Star Wars Expanded Universe has many problems with continuity. Most stem from the fact that the time period has the highest media density of any period in the Star Wars timeline, with multiple cartoon series, video games, novels, and comics packed into a three-year period. As more stories, situations, and characters are introduced, more contradictory elements appear.The most jarring of these apparent contradictions is the role of Ahsoka Tano, Anakin's young Togruta Padawan. Based on earlier Star Wars media, it seemed like the series began in 19.5 BBY and ended before 19 BBY, when Episode III: Revenge of the Sith is set. And yet there are no indications in that film or later media of Ahsoka's fate, or even of the fact that Anakin had an apprentice at all. Later adjustments to the timeline put the beginning of the series around 21 BBY, but this only raises more questions; surely Anakin's apprentice of two years would be worth mentioning, even if an apprentice of a few months could be easily forgotten.It will take a few more years for The Clone Wars to end and the timeline to sort itself out, with new books and other media addressing the continuity problems. In the meantime, fans can only speculate about Ahsoka's fate, and have come up with a number of theories. Some seem particularly likely, while others are wildly implausible.
Possibility #1: Ahsoka Dies
Evidence For: The easiest way to get Ahsoka out of the picture is to kill her. She would have to die a suitably herioc death, of course, perhaps sacrificing herself to save Anakin and the other Jedi. Alternatively, perhaps one of Anakin's reckless plans contributes to her untimely death. The subsequent self-blame might explain why Anakin never mentions her later.
Evidence Against: With the beginning of The Clone Wars set in 19.5 BBY and the series' projected run of 100 episodes, Ahsoka's death (if it does take place) must be very close in time to Revenge of the Sith. One would expect, then, for it to be at the forefront of the characters' minds. At the very least, any action on Anakin's part that contributed to her death would be carefully considered by the Jedi Council before they agreed to admit Anakin.Out-of-universe, one must also consider the show's intended audience. Ahsoka was created to appeal to a younger demographic. Killing her would be too dark for the series and would potentially alienate its viewers.
Possibility #2: Ahsoka is Expelled from the Jedi Order
Evidence For: Ahsoka's reckless behavior and inability to follow orders might lead to a tragedy, forcing the Jedi Order to expell her. She does take after Anakin, who is far more reckless -- but she has neither the sheer power nor the prophecy that Anakin has which force the Jedi Order to keep him despite anyone's misgivings. If she continues disobeying orders and mounting battle plans that kill half her men, perhaps the Jedi Order will judge her too dangerous.
Evidence Against: If Anakin's only apprentice is expelled from the Jedi Order, it will reflect badly on him whether or not it is his fault. It doesn't make sense for no one to point it out when the Council refuses to make Anakin a Master.Regardless, the Order is so desperate for Jedi that they put young Padawans like Ahsoka out in the field -- and that, in Yoda: Dark Rendezvous, they accept Force-sensitives as Padawans who would normally be sent to the Agricultural Corps, the destination of choice for failed Jedi. If Ahsoka is too reckless, that is an argument for training her better, not for expelling her.
Possibility #3: Ahsoka Leaves the Jedi Order
Evidence For: Leaving the Jedi Order would put Ahsoka out of the picture without anything so dramatic as her death and without the problems associated with her expulsion. As long as she leaves the order of her own volition, it will not reflect too badly on Anakin. Since Ahsoka has no ties outside the Jedi Order, such as family, that might make her leave, perhaps the most likely scenario is a romance that forces her to reconsider her commitment to the Jedi way.
Evidence Against: Unlike Anakin, Ahsoka was raised in the Jedi Order, and knows no other way of life. Other Jedi have left the Order -- such as Ferus Olin in the Jedi Quest and Last of the Jedi series -- but that was following a serious tragedy, something that would have a profound effect on Anakin as well. And it's hard to imagine Ahsoka abandoning her loyalty to the Jedi Order for personal reasons, especially when she knows how few Jedi are available.
Possibility #4: Ahsoka is Reassigned to a New Master
Evidence For: Reassigning Ahsoka solves the problems associated with expelling her. Perhaps the Council decides that Anakin is a bad influence on her and finds her a Master who's a bit more responsible. Or perhaps it's something even more mundane: Ahsoka is reassigned after Anakin is presumed dead, just as Anakin was temporarily reassigned to Ki-Adi-Mundi after Obi-Wan was believed dead. When Anakin returns (in this scenario), Ahsoka stays with the new master, who turns out to be a better fit for her training.
Evidence Against: The evidence against the Council reassigning Ahsoka to get her away from Anakin is the same as the evidence against her getting expelled or dying because of Anakin's mistakes: it reflects badly on him, and so should come up when he joins the Council. If she's reassigned for reasons unrelated to his conduct, however, it makes sense that the issue never comes up.
Possibility #5: Ahsoka Turns to the Dark Side
Evidence For: Ahsoka has, so far, displayed may traits similar to Anakin: recklessness, rebelliousness, strong attachments. Being Anakin's Padawan has only fueled these tendencies. Set off by the right tragedy, Ahsoka might fall to the Dark Side, foreshadowing her Master's downfall.
Evidence Against: Despite Ahsoka's flaws, there have been no hints, as with Anakin's character, of something deeply sinister yet to come. Her turning to the Dark Side would be too unexpected and unbelievable. And as always, one must return to the problem of her behavior's reflection on Anakin: surely his Padawan turning to the Dark Side very shortly before Revenge of the Sith would make the other Jedi more inclined to keep an eye on him.
Possibility #6: Ahsoka is Knighted
Evidence For: The Jedi are stretched thin during the Clone Wars. Anakin became a Knight without undergoing the customary trials. Perhaps a talented young Padawan such as Ahsoka might get pushed through to Knighthood earlier than usual in such circumstances.
Evidence Against: Remember that The Clone Wars takes place within a period of six months, and Ahsoka is only 14. Even if she'd been a Padawan for longer than a few months -- and even considering the show's young audience -- she'd be far too young to become a Knight. In fact, there are Padawans older and more experienced than her, such as Bariss Offee, who have yet to be Knighted.In addition, training a Padawan to Knighthood is one of the biggest steps towards becoming a Jedi Master. If Ahsoka becomes a Knight, the Council would have little reason to deny Anakin the title of Master in Revenge of the Sith.
Possibility #7: Ahsoka Goes on a Mission
Evidence For: Sending Ahsoka away temporarily during Episode III would solve the problems associated with the more permanent ways of removing her. If she is sent off on her own mission at the end of The Clone Wars, that would work to show how her character has matured. Anakin doesn't mention her during Revenge of the Sith because nothing happened to her -- she's just away temporarily. In this scenario, perhaps she dies during Order 66 -- or perhaps she and goes into hiding, like with Obi-Wan, Dass Jennir, and a number of other Jedi.
Evidence Against: Dying off-screen during Order 66 would be an anticlimactic end for such an important The Clone Wars character. If she survives, though, there's plenty of future media to address what happened to her.
Possibility #8: The Clone Wars is a "What If?" Story
Evidence For: Here's where we get into some more bizarre, out-of-universe explanations for the events in The Clone Wars. If the series takes place in an alternate universe, perhaps in the real Star Wars universe, Ahsoka does not exist. To drive the "What If?" point home, perhaps something happens in The Clone Wars that prevents Anakin from falling to the Dark Side. If that happens, the series can continue past the time of Episode III without worrying about how to get rid of Ahsoka.
Evidence Against: There have been several "What If?" stories in Star Wars, published under the label Infinities. The Clone Wars has no such label, and as such it is considered canon. In fact, because of George Lucas' more direct involvement in the series than in other parts of the EU, it is considered a higher level of canon than the books, comics, and other media. With other stories referencing the characters and events of The Clone Wars, declaring the series AU would cause too much confusion in the timeline.
Possibility #9: The Clone Wars is an In-Universe Holodrama
Evidence For: Making The Clone Wars an in-universe story would clear up many discrepancies. Some of the series could be canon, because it's based on historical events, but other parts might be full of artistic license and other historical inaccuracies. Under this theory, perhaps Ahsoka doesn't really exist in the Star Wars universe, and she was invented to make the holodrama attract children; or perhaps her character is based on a minor, unimportant character whom Anakin temporarily trained. Timing matters less, too: consider M*A*S*H, where the Korean War lasted for eleven seasons.
Evidence Against: Although there is a precedent for EU works as in-universe documents, they are always clearly marked as such. Luke Skywalker and the Shadows of Mindor, for example, ends with a frame story where Luke Skywalker complains about the inaccuracies in the preceding tale. There are no such clues in The Clone Wars, and so suddenly declaring it in-universe fiction would be an unsatisfying cop-out.That's not to mention the fact that, in the Star Wars universe, Anakin is remembered not for his heroism in the Clone Wars but for his atrocities as Darth Vader.No matter how much foreshadowing goes into The Clone Wars, an in-universe show featuring the heroic exploits of Darth Vader feels a bit like the Star Wars equivalent of Young Hitler's Adventures in Art School.
So What Really Happens to Ahsoka?
Fans have a long wait ahead before The Clone Wars ends and the writers reveal Ahsoka's final fate. No matter how the story ends, a great many people will inevitably be disappointed. Perhaps the best way for Ahsoka to go, however, would be a final confrontation with her former Master after he becomes Darth Vader. It will only show the extent of Anakin's transformation when he slaughters her mercilessly along with the rest of the Jedi.