So basically I'm writing a story set in a magical world where there are separate covens, each with different mission statements (there is one for those who want to be healers, one for those who want to care for magical animals, etc.). There are also some evil covens who wish to spread their reign of terror. Unfortunately, it's very similar to the anime Fairy Tail, which is set in a fantasy world and involves guilds instead. How can I change it to be different? Please help?
There are no original story ideas. It has all been done before. Any originality lies in the telling, not in the story idea.
And, the publishing industry cares about originality about as much as the pizza industry does. Most customers do not want an original pizza. They want the same pizza they always order served hot, fresh, and on time. The publishing industry wants writers who can deliver familiar stories hot, fresh, and on time.
What is wanted, therefore, is not original ideas, but fresh takes on familiar ideas whose marketability is well known.
It's also similar to Harry Potter and Divergent. Just as there was a rash of vampire/paranormal YA fiction after Twilight, there's currently a run on quasi-facist highly and arbitrarily segregated dystopias. Art reacts to life.
Mark is right. Don't worry about whether it's been done before. Write your story and work on doing it right. You can always get feedback from beta readers about whether it feels too derivative and then polish world-building details in later drafts. Get it written now.
The things about rip-offs is that it largely comes down to the details, which, unfortunately to an internet Q&A site like this, is largely unavailable. With that being said, I should stress that there is a difference between having parallels to and inspiration from something, and ripping it off.
I think that many authors have encountered that intrusive thought - will people think I have copied X and subsequently, will I be judged for it? Allow me to share this particular advice: most people will only call rip-off if your story completely lacks its own identity. As I wrote 3 sentences back, this identity usually will exist in certain details. Nevertheless, reimaginings and reinterpretations of something else probably won't get you called-out for being unoriginal. Contrarily, trying to reimagine something deep and complex, and doing it well, is probably as difficult as coming up with something original. People tend to judge an experience such as music, book, novel, film and video game on the emotional impact a lot more than on its plot-structure and similarity to other things. Hence, one can conclude this: if you try to recapture the emotional value of some experience (e.g. Fairy Tail) and you do it poorly, this is when you will likely be called out for being a cheap and unoriginal.
On top of the above, I should add one other thing. In a previous question, I stated something along the lines of "there are a few truly bad ideas, only poor executions of ones." One truly bad idea is to try and out-predict your readers. I like to call it the "internet celebrity fallacy." So many internet celebrities try to behave and do things in a certain way, because they believe it is what their fans want. As a consequence, they come across as artificial and cringeworthy, and instead get more bile and hatred (more so than the internet usually attracts, anyway). Something similar applies to novel writing: if you try to specifically do something in order to coerce your readers into thinking something - for example, trying to artificially distance yourself from Fairy Tail - and worse, try to hide it, that won't warrant any positive criticism. The remedy to this predicament is: don't worry about it. If you write a good novel, readers are going to respect that, even if some parallels to what inspired the novel in question are pretty obvious.
The Witch and Friday the 13th can both be summed up as, "A group of people are isolated in the woods and a monster kills them one by one." No one would say they're the same movie.
As long as you put enough of yourself into your story you should be fine.