Naruto’s Biggest Plot Hole? The Villain Itachi Should Have Killed

Every fandom has that one mystery you can argue about forever. For Naruto, it is this: why didn't Itachi Uchiha just take out Danzo Shimura when he had both the motive and the means? The guy wiped out his own clan in the name of peace, but left the one power broker who engineered half the chaos still breathing. It is a choice that never quite sits right.

The head-scratcher: Itachi lets Danzo live

Itachi is framed as Konoha's ultimate realist: a prodigy who saw war up close, understood the village's rot, and still decided protecting it was the only path. When the Uchiha and the village brass were headed for a collision, he chose the village. Cold. Calculated. And then he stops short with Danzo, the same operator pulling strings inside the shadows to inflame that conflict in the first place.

Danzo was not just another elder in a robe. He was the backroom architect, the one Itachi took orders from in the run-up to the massacre. If there is a single moment that should have flipped Itachi's switch, it is what happened to Shisui.

Shisui: the pivot point

Shisui Uchiha was Itachi's best friend and moral ballast. He believed in a nonviolent solution and had the rare genjutsu to make it happen. Danzo ambushed him, took his Sharingan, and Shisui died. That is the domino that never stops falling. By any practical metric, Itachi had the capability, the justification, and a window to remove Danzo right there. He did not. And that choice is the one that feels wildly out of step with the rest of his logic.

Why sparing Danzo was a huge gamble

Leaving Danzo alive did not just bend Itachi's code; it endangered the very peace he was trying to preserve. Danzo kept operating, kept manipulating, and the long tail of that decision reaches into every corner of the story. You could argue the meta answer is that Masashi Kishimoto wanted Danzo around for later arcs. Inside the narrative, the generous read is that Itachi's idealism and faith in the village structure dulled his instincts at the worst possible moment. Either way, the risk was enormous.

Sasuke finishes what Itachi did not

When Sasuke finally gets Danzo alone in Naruto Shippuden, it is the payback the story has been lining up for years. Sasuke wins. On paper, that settles the score. In practice, it is too late to fix anything that mattered.

• Shisui is gone.
• The Uchiha clan is gone.
• Itachi is gone.
• Danzo's machinations have already scorched multiple generations.

The uncomfortable truth about a legend

Itachi is one of anime's great tragic figures, and he earns that status. But legends still miss, and this is the miss. He sacrificed everything for stability, then left the one man undermining that stability untouched. Maybe that tension is what makes his story feel human: even a genius can misread the one variable that matters.

So what do you think? Should Itachi have eliminated Danzo when the Shisui incident blew everything open, or is sparing him consistent with Itachi's peace-at-any-cost mindset? How would you rewrite that turning point?

Naruto and Naruto Shippuden are streaming on Crunchyroll.