When Anakin Skywalker questions the orders of a Republic Admiral during a Star Wars comic set during the Clone Wars, it reveals that Qui-Gon Jinn's moral philosophy had a deep impact on the young Jedi. Unlike other iterations of the character, the comic Star Wars: Age of Republic - Anakin Skywalker fleshes out Anakin's disagreements with how the Clone Wars were fought.
The Clone Wars was a three-year battle between the Galatic Republic and the Separatists. One of the key differences between both sides was that the Galactic Republic used human clone armies created on Kamino and commissioned by the long-dead Jedi Sifo Dyas. Contrarily, the Separatists commissioned a vast army of Battle Droids that had no soul and were meant to simply follow orders. Additionally, the Galactic Republic had an espionage service that partook in covert missions to gather intelligence on the Separatists. But this also put the Republic at risk of being fed misinformation as a trick so they would wrongfully attack innocents.
Star Wars: Age of Republic - Anakin Skywalker is written by Jody Houser with art by Cory Smith and Wilton Santos. The comic starts by showing Anakin's perspective on a battle between Republic and Separatist forces in the Corvair Sector. When Republic Admiral Yularen proposes to blow up an entire foundry full of droids on the nearby third moon of Kudon, Anakin realizes that the foundry's human workers will also be inside. The result of the attack, he says, will be "killing everyone inside. Living beings, not droid soldiers." The young Jedi opposes this plan, reminding Yularen that these beings inside "aren't soldiers. They're workers." While Anakin is fine destroying droids, his morality does not agree with the idea of ending the lives of those who can feel emotions and make judgments about their lives. Additionally, as workers these beings are contracted to perform their job duties, whereas soldiers are prepared for battle and know their deaths on the battlefield are a possibility.
When discussing the matter with Obi-Wan Kenobi, Anakin says, “Isn’t that the whole reason the Jedi are a part of this war? To save lives?” At the end of their conversation, Anakin’s facial expression expresses his anger when he says that “slaughtering people like this is just wrong.” Anakin reiterates Qui-Gon’s belief that the Jedi have lost their way because their actions seem more aligned with fighting against the Separatists than saving lives across the galaxy. Anakin’s disagreement with slaughtering people in the name of a successful war effort echoes Qui-Gon’s opinion that the Jedi are more focused on acting as a tool of war for the external Republic rather than focusing on the internal Order’s duty to every planet.
By challenging Admiral Yularen’s direct orders, Anakin’s actions are more aligned with the Jedi Order’s original mission to act as peacekeepers throughout the galaxy rather than blind soldiers just following orders. Much like Qui-Gon Jinn, Anakin Skywalker’s adherence to the Jedi Code enlightens him about the controversial aspects of war. It shows how, even though Palpatine was already grooming him, the good in him remained fixed through his morality. Ironically, Anakin’s disagreement with killing innocents contradicts Darth Vader’s later slaughter of the Jedi and younglings during Order 66, which he admits is his darkest act. This Clone Wars conflict exemplifies the light within Anakin Skywalker’s morality during his struggle with the dark side and how it resembles Qui-Gon Jinn's beliefs throughout the Star Wars franchise.