The Worst Crime The Akatsuki Ever Committed In Naruto
While they aren't often seen until "Naruto: Shippuden," the Akatsuki are certainly one of the most formidable villains in both "Shippuden" and the original "Naruto." They may be mostly absent from the first half of the story, but their influence can still be felt. For the Akatsuki, whether we see them or not, they are always there, subtly pulling the strings and altering events to accomplish their ultimate goal.
"Pulling the strings" and "altering" events may be very generous terms, mind you. In some way or another, the Akatsuki are responsible for most of the horrible things that happen in "Naruto." It's one of their highest-ranking members, Tobi, who unleashes the nine-tailed fox on the day that Naruto is born, forcing the Fourth Hokage to seal the fox inside his own son and ultimately kicking off the events of the entire series. Likewise, it's those who manipulate the Akatsuki — Madara Uchiha and Black Zetsu — who summon the series' main antagonist, Kaguya Otsutsuki.
Releasing Kaguya and the nine-tailed fox, however, are only some of the lesser tragedies that the Akatsuki are connected to. Truthfully, the worst crime the Akatsuki ever commit is done by an entirely different leader. Because while Madara, Tobi, and others are certainly evil, they're not quite as good at inflicting suffering and pain as, well, Pain.
Pain single-handedly destroys the entire Leaf Village
For a long time, the Akatsuki is not run by Madara and Black Zetsu. While these two certainly manipulate and control the Akatsuki, it's a man named Nagato and his friends who initially found the group with the goal of bringing peace to the world. Unfortunately, the noble beginnings of the Akatsuki don't last long. After the death of their first leader, Yahiko, Nagato takes control and rebrands himself as Pain, for the only way he believes people can learn to live in peace is by experiencing pain.
With the power of his Rinnegan, Pain becomes one of the most powerful people on the planet. Many, because of his Rinnegan, think he will become the next Sage of Six Paths, a new hero who will bring peace to the world. Instead, Nagato possesses six warriors to create the Six Paths of Pain, each of which has its own unique power. One of these, the Deva Path, is made from Yahiko's body and possesses the ability known as Almighty Push.
Using Almighty Push, which works like a "Star Wars" force push on steroids, Nagato instructs people on the meaning of pain by destroying the Hidden Leaf Village, killing thousands of people. What is once a bustling and vibrant city becomes a flattened crater of rubble and bodies. By almost every margin, it's the single most destructive and horrific action taken by the Akatsuki.
It's okay though, because Nagato can just take it back
At the end of the day, "Naruto" is an optimistic anime, so it's no surprise that by the end of his story, Nagato ultimately fails in his goals. After Naruto defeats the Six Paths of Pain in the ruins of the Hidden Leaf, he finds and visits Nagato's real body. As is common between Naruto and his opponents, the two have a nice little chat about Nagato's backstory, how his life went awry, and how he started off with noble intentions. Thanks to this talk, the two enemies gain a better understanding of each other, and Naruto manages to convince Nagato that there are less sadistic ways to broker peace in the world.
So, Nagato undoes what he did to the Leaf Village. His Six Paths of Pain may not be able to rebuild all the buildings, but with the Outer Path's Samsara of Heavenly Life technique, Nagato can resurrect all of the people he kills when he flattens the Hidden Leaf — and that's exactly what happens. Having defeated the Akatsuki, Naruto finally gets the respect and recognition of the entire Hidden Leaf. If only this is the last of what the remaining members of Akatsuki have up their overly-large sleeves.