I have never seen a game fail so hard at retelling a story from the source material as I have with Naruto Online.
The story jumps all over the place, there is very little explanation for what is occurring on screen and most of the time what is occuring on screen has nothing to do with what occurs immediately after. The game doesn't even get the story right despite copying the fact that they only have to copy the manga or anime or the Naruto games. The missions jump from one part of the story to the next with only the barest of material to vaguely link the story instances together, even though that is frequently missing too. Sometimes the story loops back on itself and very frequently events happen without any context or explanation. What made the original story so good was the fact that it made the viewer become emotionally attached to the characters, to their plight, to understand their hopes and dreams, to become emotionally invested in the story. But you don't do any of that because your story is a completely disjointed, undeveloped, poorly translated mess. You don't bother trying to flesh out the characters, to understand the story, to develop a connection between the story and the player. You simply jump from one event to the next and hope that the player's memory of the anime/manga/better Naruto games are enough to carry them forward.
For example, what made the final fight between Naruto and Sasuke of pre time skip Naruto so good was the fact that it was so emotionally charged. These were characters that the viewer had become attached to after watching them develop for years. It wasn't the animation that carried the day (although it was quite good). It was the viewer's connections to the characters themselves that made the last fight so good. The viewer sympathized with Sasuke's need to become stronger at any cost in order to avenge his family's death by killing his brother. The view wished that Naruto would succeed in stopping Sasuke because if Sasuke left to join Orochimaru they'd be losing someone they themselves had become attached to just like Naruto. No matter who won the viewer knew that everyone would lose, including the viewer because of the attachment that the series developed in the viewer. In your game there is no attachment because we never ever come to learn about the characters, we never learn about their hopes and dreams and desires. We never come to learn what drives them, what makes them the characters they are.
Rather than taking the source material and then determining how the story would change when a fourth ninja was added to team 7, you pretend that team 7 still only consists of Naruto, Sasuke and Sakura despite the fact that the player's interactions with the "story" prove that there is now a 4th member. For example the game pretends that the time you kicked Deidara's * during the mission didn't happen and immediately shows Deidara *ing up the sand village and kidnapping Gaara even though this couldn't happen because you just killed Deidara not seconds before so it wouldn't be possible for Deidara to beat and then kidnap Gaara as Deidara was now dead and couldn't kidnap anybody. That was the entire point of that fight (and it didn't work in the anime either because there is no way that Gaara would have taken so long to beat Deidara, there is no way that some clay worms could work their way through a shield made of sandstone when that sandstone was completely encasing the worms and preventing them from moving, and no way that Gaara's sand which was so slow it couldn't catch up to Deidara flying at 20 mph but could somehow spread faster than the speed of Deidara's exploding clay bomb which was expanding at the rate of several hundred miles an hour).
If you aren't going to recognize the player's efforts and inputs, then don't have them. Just show the player arriving just as Gaara was defeated and being kidnapped, have the player try to rush to get back Gaara but be blocked by some throwaway ninjas while Deidara gets away. But that would require that the game developers put actual work and thought into the game, something which they clearly hate doing considering what a sorry mess the "story" is in and how the translation would be bad even for Google translate. Was the story translated from Chinese to German and then from German to English because I don't see how a story translated directly from Chinese to English could possibly be this bad. Creating a story requires connecting events together in a way that logically flows and progresses, something which Naruto Online consistently fails to do. In the words of Transformers: Revenge of the Fallen, one of the worst movies of all time, a story consists of "Beginning, middle, end. Facts, details. Condense: Plot. Tell it!" If a Michael Bay Transformers movie can figure out what is needed to make a good story, what is your excuse?