The Akatsuki are some of the most iconic villains not only in Naruto but in all of anime. They're everything that a good villain should be; they're mysterious, intimidating, powerful and complicated characters. However, before the Akatsuki was a group of world-renowned criminals, they were a group of heroes. Despite their fall from grace, a small piece of the Akatsuki's original goal still existed in their corrupted group, making their downfall all the more tragic.
The ninja world has been plagued by war and conflict for the majority of its history. One of these wars created three orphans from the Village Hidden in the Rain, who were left to suffer and languish in the destruction of their home. These orphans, Yahiko, Konan and Nagato, were taken in by Jiraiya and trained to defend themselves against the dangers of the world. Jiraiya shared his dream of peace with them, giving them hope that the war destroying their country would one day end. This hope inspired Yahiko to create an organization dedicated to ending the war ravaging their home: the Akatsuki.
The Akatsuki was not originally a militaristic group. They did not use violence to eliminate their opponents but instead attempted to create peace through pacifist means. Under Yahiko's leadership, the Akatsuki gained more supporters and recognition for their activism. If the group had been allowed to continue without interference, they would probably have succeeded in ending the war and would have been regarded as heroes.
However, because of the manipulation and deception committed by Obito, Madara and Black Zetsu, that original dream became corrupted. The leader of the Village Hidden in the Rain, Hanzo, viewed the Akatsuki as a threat to his power and worked with Danzo to eliminate them in an ambush. During that ambush, Yahiko killed himself to protect Nagato and Konan. He hoped that the two of them would carry on his dream and the goals of the Akatsuki.
After this event, Nagato's worldview was shaken. He still wanted to live in a peaceful world, but he no longer believed that it could be done without violence. Obito and Black Zetsu reinforced this idea and convinced him that the world could never be at peace without the use of force. Those with power would always enact pain and suffering on those weaker unless they were made to experience the same pain. Nagato would achieve peace through war and violence, uniting the world through shared anguish and trauma. With this new ideology, Nagato created the new Akatsuki, a group of villains dedicated to that goal.
The Akatsuki would repeatedly be usurped and manipulated by outside forces. Obito, Madara and Black Zetsu would use the organization for their own purposes. Yahiko's dream of peace would continue to be diluted and distorted with each new manipulator. The Akatsuki had been transformed into a grotesque mockery of what the original organization stood for.
Nonetheless, the tragic story of the Akatsuki does end with a happy ending. The group was redeemed by Naruto Uzumaki. Before their deaths, Nagato and Konan both trusted Naruto to carry on Yahiko's dream of peace. They believed that Naruto understood the importance of peace and could succeed where they had failed. When Naruto united the ninja world during the Fourth Shinobi War and created a lasting alliance, he didn't just accomplish his goals, but the goals of the original Akatsuki created by Yahiko all those years ago.