WARNING: The following contains spoilers for Star Wars: Age Of The Republic - Qui-Gon Jinn #1 from Jody Houser, Cory Smith, Walden Wong, Java Tartaglia and VC's Travis Lanham.
In Star Wars lore, Qui-Gon Jinn is known for his rebellious ways. Sure, he's a Jedi Master operating just outside the reach of the council, but he often breaks rules when needed because he understands rules usually end up in absolutes, and that's the Sith way. Of course, being a rebel like this also allows him to do things with his signature style and flair, allowing quick results when it comes to solving trade disputes for the Republic.
Jinn knows what he enlisted for, but, simply put, he wants to do things his way. It's a compromise the Jedi Council is willing to work with because Qui-Gon never really fails at any task he's given. However, in Star Wars: Age Of The Republic - Qui-Gon Jinn, we learn exactly what his deepest, darkest secret is regarding the Jedi, and how conflicted he was when carrying out these missions.
Marvel's one-shot paints him in a light similar to how we saw Liam Neeson portray the character when he debuted in The Phantom Menace. Qui-Gon's rescuing an important political figure with Obi-Wan Kenobi on the lush planet Bri'n, taking her back to Coruscant until the Trade Federation resolves the war there. En route, the target asks Qui-Gon why they simply don't use their Jedi powers to kill the soldiers involved in the hostile takeover, but he makes it clear they're not soldiers. Or, at least, he tries to fool himself and Obi-Wan into thinking that, which leads to the person they're escorting calling them cowards.
Subsequently, in a heartfelt one-on-one with Yoda, Qui-Gon admits that there's regret in him joining the Order. Yoda tells him they're trying to create a better galaxy, but Qui-Gon feels like they're in the belly of the beast and at this point, the secret spills out: he feels like a weapon deployed for the Republic and corrupt politicians. More so, there's PTSD visible as his guilt manifests from previous kills.
Yoda doesn't want Jinn confronting the council with these concerns and sends him off on a therapeutic journey. Qui Gon gets in his jet, closes his eyes and lets the Force randomly pick a planet for him to meditate on. When he arrives at yet another lush world, he goes from being in awe at its beauty to having what seems to be a hallucination of death, foreshadowing the fall of the Jedi. The story, appropriately named "Balance," then sees him centering to his mind by relying on the Force before heading back to Yoda.
He returns recharged, but it's clear Qui-Gon can no longer tell the difference between the Jedi and the Sith, as both are weapons trying to establish the rule of a certain regime. Nonetheless, he buries the feelings of being a murderer deep below because he wants to honor Yoda's tutelage and groom Obi-Wan to become better than him. Little does he know the entire fate of the cosmos will be changed when he meets a young Anakin Skywalker later down the line, paving the way for the young man to become Darth Vader.
What's even more noteworthy about the master's crisis of faith here is it's very similar to Luke Skywalker's in Rian Johnson's Star Wars: The Last Jedi. There, Luke turned his back on the Jedi Order, even renouncing the Force itself. But as Qui Gon makes perfectly clear, they serve the Force, not the Jedi Order, which Luke learned later on and then passed to Rey as he tried to mentor her.
It's poetic seeing Qui-Gon understanding that the Force is their moral compass and it should be a tool for everyone, not just Jedi and Sith. But it's tragic knowing he'd fall to disciples of the Dark Side, and decades later, so too would Luke in trying to embed this philosophy within the next generation of heroes.