Well I believe a few people have already mentioned this in this thread, but good advice always bears repeating. There are no new stories, ever! Avatar (the James Cameron film) was nothing more than a sci-fi retelling of the plight of Native Americans, but it was told with such an interesting setting and characters that it became a huge hit. Star Wars was nothing more than a Cinderella story when you get right down to its core. Do not let the idea of writing similar works skew you from pursuing your passions as a writer, simply embrace your story and mold it into something you truly believe in. Haters are going to hate, generally because they will not have accomplished what you have brought to life with your creative works. My best advice is to read Joseph Campbell's "The Hero With a Thousand Faces" cover to cover and use it as the backbone of your plotline. Whether the story you have mimics some other work of art (which it is going to) the Hero's Journey is never a bad baseline to use.

Mass Effect 3's ending was a literal criminal act. Cmdr Shepherd is presently serving time in Lompoc for failing to deliver the goods.

That being said, originality isn't really usually possible. If your story is something that you yourself have never heard of then it's probably original enough. Finding out that some idea you came up with already exists in a popular game should really be an encouragement because it means that people like the idea! Players will usually get miffed if they feel like a promise you made to them was broken. In the case of ME3 it was the promise that the things you did in the game actually mattered. (whoops)

In the case of plot, as long as the story is cool and the game is fun to play then people don't usually get hung up on how original it is unless they're just having the knee-jerk deconstructionist reaction that's common to modern society. Some people will sit down and play a game for hours on end, then take a break to complain about how awful it is and go back and play it for a few more hours. As long as you're not just throwing a new paint-job on someone else's work (that's M$'s job!) you should be quite alright.

If you're looking to get a pat on the back from a customer base then this probably isn't the right industry for you.

If you're looking to make something that people can enjoy then just ignore all outside factors and go for the gold.

Saying there are only 7 stories in all of literature is like saying there are only three colors in all of art.

Saying there are only 7 stories in all of literature is like saying there are only three colors in all of art.

And yet some really smart people insist on saying it! Depending on how coarsely the 'basic' plots (and plot is a more accurate word here than story) are defined, people have outlined anywhere from 36 to just one, with 7 being the most-quoted number. The exact number is irrellevent, as they are all effectively zero compared to the great variations of detail that we call stories (again, 'plot' is a better term than story to describe the basic enumeration).

Color and form in the visual arts are akin to detail in the literary -- an apt analog for the basic literary plots in the visual arts would be the subject (in abstract art, the subject might be form and/or color itself).

But if you want you can split hairs all day long, but then you start to sound like two teenagers arguing about whether band X is really metal-core-screamo or screamo-core-metal.

Saying there are only 7 stories in all of literature is like saying there are only three colors in all of art.

There are only a few colors in art. Some of those colors are even imagined! Pink doesn't even really exist. The rest are shades and hues of those basic colors. There are even limits on what colors look good with other colors, further reducing possible color combinations. There are also limited techniques, poses, angles, and composition rules that actually look good, further reducing your options if you want to produce great work.

There are only a few basic story types, everything else is splitting hairs. And that's fine with me! Stories also follow pre-defined structures to work out for the best. Most stories follow a basic 3 act structure, and characters are a mixture of predefined tropes. Only the names and places change.

The problem is I've devloped a crippling fear of writing due to discovering that a key element to my game's backstory is slightly similar to a big AAA RPG's.

It is interesting that you mentioned it.
Watch the recent video about your problem in the VlogBrothers' channel.

unfortunately, whatever you do, you'll find always people criticizing you. in theory, 50% will love you, and 50% will hate you. Then the percentage changes depending many factors, the actual trends in entertainment business, the advertising, etc etc

the cool thing is that also if you make something mediocre, you'll always find fans... it's statistical. how many stupid games became famous games???

so the best reviewer is yourself and your conscience. If you feel ok with your work, go ahead. Maybe change something of the plot to be 99% sure anything will go right. If you fear something is wrong, just change the plot and relax. but always follow your intuition, never the others one.