This style of a story is very common in shonen anime/manga. So it's not a big surprise that this would have reminded you of naruto, but if you had a more vast knowledge of anime, other than naruto and bleach, you would have noticed that this is repeated in a lot of series.
First 20 % of the series, bad guy doing bad stuff, totally 100% against the protagonist. This first part of the series lets you make your impression on the bad guy, that in fact he is bad and his intentions are bad, and you don't like that because you want the character that is shown in front on the cover to win.
Reaching 40 % into the series, after some shenanigans between the characters ( bad and good ), the series finds itself to a point where it shows a soft spot on the bad guy (remember, you already made the impression he is bad in the first few episodes or first season, depends on the series), flashbacks of the bad guy start showing, and it feeds you the impression that maybe his motives are somewhat justified, and now you start having mixed fillings, you start questioning yourself, maybe you we're wrong about him.
Beyond 40% towards the end, after a few more shenanigans and more information feeding, you start to root for the supposedly bad guy, and can't wait for them to maybe join forces, because, big surprise, the REAL bad guy shows up (because, seriously, how would the series would have continued otherwise ?) and he is super strong, he may look OVERPOWERED.
At 80% in the series, looks like the bad guy that is not actually bad ( your eye-candy, to be exact ), the guy that no one understands and no one knows what he has been trough, starts clashing with the boring main character, but hey, looks like they reach and understanding, they need each other to fight the super strong villain. So this is the point where they still don't really get along but somewhat work together, and other shenanigans occur.
REACHING THE FINAL PART OF THE SERIES, all plans have failed, the teams are all down, but wait, the bad guy who is actually just misunderstood, has something up he's sleeve (well, maybe at this point he is already shirtless, you know, for the eye-candy, so no sleeves ).
>VILLAIN IS LAUGHING, HE THINKS HE IS TOO POWERFUL, AND THE UNIVERSE/GALAXY/EARTH/COUNTRY/CITY/SCHOOL ( I don't know, pick one...) BELONGS TO HIM NOW.
> BADGOOD GUY STANDS UP, LONG SPEECH STARTS, MOOOAARRR FLASHBACKS, AND NOW EVERYTHING ABOUT HIM IS REVEALED.
> FIGHT STARTS, HE TELLS THE OTHER TO LEAVE NOW
> "BUT SASUNARUZAKA-SAMA-SAN-CHAN, WE WILL NOT LEAVE YOU, WE CARE ABOUT YOU"
> "NO YOU FOOLS, LEAVE NOW! (STARTS CHARGING BIG ENERGY / PLANTS TIME BOMB / SETS THE SHIPS MAIN COMPUTER TO SELF DESTRUCT, because, hey, all of the ships have an option to self destruct.
>EVERYONE LEAVES IN TEARS, THE BIG BOOBED GIRL THAT GAVE HIM SEXUAL TENSION TROUGH THE SERIES NOW SAYS HE LOVES HIM (yeah, i'm about to kill myself and now you tell me, thanks bitch)
> THE VILLAIN REALIZES WHAT IS GOING ON "YOU STUPID EARTHLING, YOU WILL KILL US ALL !"
> MOAR SAD FLASHBACKS, MOAR TEARS
> IT ALL CAME TO THIS SCENE, CUE SMUG LOOK ON THE BADGOOD GUY WHO IS THE CHAOTIC GOOD CHARACTER IN THE STORY, HE SAYS A SMART CATCHPHRASE.
..
....
...episode ends.
NEXT WEEK STARTS A NEW FILLER WITH ALL OF THEM IN SCHOOL AND THE VILLAIN GALACTICAMARU AS THEIR SPANISH TEACHER, MOOOARRR SHENANIGANS !
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