It took some time, but Star Wars has officially explained why Qui-Gon Jinn was the only Jedi who could have saved Anakin Skywalker - because only Qui-Gon learned the truth about the Dark Side that Obi-Wan, Mace Windu, and even Yoda never realized.
To be clear, Qui-Gon Jinn is still responsible for taking the risk of recruiting and training Anakin Skywalker, setting him on his path to becoming Darth Vader. But in a new one-shot comic book revealing Qui-Gon's crisis of faith long before Episode 1, the Jedi Master's doubts and true intentions are finally explained. Qui-Gon didn't fail to notice the Dark Side boiling up inside of Anakin Skywalker: he believed that darkness was exactly what was needed to bring balance to The Force. Showing once and for all that Anakin could have brought peace to the galaxy... if Qui-Gon Jinn had trained him.
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Qui-Gon Realizes The Truth of The Dark Side
If you're a staunch believer in the version of The Force explained by the Jedi, you've heard it already: light side good, dark side evil and terrible. But for all their talk of "balance" the Jedi Order of the Star Wars movies had grown rigid in their prejudice. And in the pages of Star Wars: Age of Republic: Qui-Gon Jinn, the Jedi's crisis of faith long before The Phantom Menace is finally shown. Not to overstate it, but Qui-Gon seems to realize what no other member of the Jedi Council is noticing: that they have lost their vision. And to get his back, he leaps blindly into hyperspace with only The Force to guide him, and accepts the lesson it has to teach him.
On an alien world teaming with both life and deadly, "dark" growth, Qui-Gon communes with The Force. Sensing both the life-giving Force and the darkness to balance it, he awakens from his vision to see that the darkness has been driven back. Light triumphed over it, returning true "balance, but through a means beyond conflict." The lesson sticks, and Qui-Gon returns to the Order keeping this knowledge to himself. The Jedi believe the Dark Side to be resisted by any means necessary... but only in the face of darkness can light restore the balance. A principle that clearly occupies Qui-Gon's mind when discovering a small slave boy on a planet called Tatooine.
Qui-Gon Chose Anakin For His Darkness & Light
It can't be overstated that this experience, this crisis of faith must force each Star Wars fan to re-contextualize every decision Qui-Gon makes when introduced in Episode 1 (it left a mark, which means his character was certainly doing the same). The lesson taught by The Force was clear, so when he, of all possible Jedi, happened across a boy conceivably born of The Force itself, Qui-Gon knew it was no accident. As he tells the Jedi Council in Episode 1, "It was the will of The Force, if that I have no doubt."
Which is where the prequel must now be re-assessed. Because when Qui-Gon confirms that he believes Anakin Skywalker is the One prophesied to "bring balance to The Force," he and the Jedi Council are imagining two different victories. For the Council, it means The Force has produced a champion to vanquish the darkness, leaving only the light. While Qui-Gon's encounter with The Force has shown "balance" to be the acceptance of darkness, so that light might overcome it. The Council senses the potential for the Dark Side in Anakin, and views it as a threat. Qui-Gon would have sensed the same, but understand Anakin's potential for darkness was the entire point of The Force's lesson (and by extension, the prophecy).
If Qui-Gon had lived to train Anakin himself, that lesson would almost certainly have proven true. Because by that point, even Qui-Gon had come to realize what Anakin eventually would: that the Jedi had lost their way.