Author's Note: Unfortunately, some people have failed to realize this: This trilogy takes place in a quasi-steampunk alternate Equestria, where tensions are much higher, and as such, weapons technology has progressed much further. Sorry to have to post this, but Equestria Daily rejected this based on 'believability issues', and I'm still a bit bitter about that.
When Unicorn extremists assassinate the twin Princesses and decimate Canterlot, Equestria falls apart at the seams. Each of the three races gathers their own and declares war on one another in a desperate bid to achieve ultimate dominance - as well as control over the fabled Elements of Harmony.
Rainbow Dash is now a member of the Wonderbolts, who have been assimilated by Pegasus military leadership and converted into a special operations task force, trusted with only the most insane and dangerous of objectives. Fire follows Rainbow Dash as her conviction, strength, and allegiances are tested time and again, and as she is forced to make choices that could seal the fate of those she loves - or of the Pegasus race as a whole.
Note: This trilogy takes place in an alternate universe, where Equestria is at a significantly higher technological level than in the show (televisions, explosives, advanced firearms etc.) and racial tensions between the three pony races were much higher to begin with. I felt the fundamental differences between the show and this story spoke for themselves in regards to Fire taking place in an alternate universe, but that clearly wasn't enough for some people, given a few of my readers have gotten after me about the technology level. Hopefully I won't have to address this again.
This is part one of a trilogy; you can find the latter parts here.
Part Two, Vengeance:
http://www.fimfiction.net/story/45457/Vengeance-%28Harmony%27s-End-Part-2%29
Part Three, The Cross:
http://www.fimfiction.net/story/45606/The-Cross-%28Harmony%27s-End-Part-3%29