In Naruto, the Akatsuki is the most powerful rapatannin organization on the planet

While Lapatanin (evil ninjas) usually act as independent criminals

Akatsuki unites with a common political goal. Far from being a gang of runaway thugs

this is a full-fledged terrorist organization with high goals and the potential to achieve them

 So Akatsuki is used as the main villain in both Naruto and (much more) Naruto: Shippuden.

Naruto eliminates Akatsuki after leader Payne is defeated, but the group still leaves a lasting impression on the world

around them. Each member was one of the most dangerous ninjas in the world, and their actions resulted in considerable death and destruction.

Defeating a single member often requires the efforts of multiple shinobi on Naruto's side..