Twilight Sparkle is dead. She died in battle, fighting to preserve the uneasy union on United Equestria between the pony races of old Equestria and the space ponies of Unicornicopia.
But in the wake of Twilight's death, the harmony she strove for has not endured. Using their control of the might armed organisation Starfleet, the Unicornicopian grip upon the land has only gotten tighter. Celestia is isolated, Twilight's friends are scattered, across the stars millions live or die at the whim of the Grand Ruler and his proconsuls.
Project Sentinel is the next step in the evolution of Starfleet, a perfect defence against a hostile universe: clone soldiers created from the DNA of the very best that ponykind has to offer. One such clone, Eve, is a physical copy of Twilight, with enhanced strength and none of the pesky moral qualms that made the real Twilight so annoying for Starfleet to deal with. When Eve, together with a small group of fellow clones, breaks free to search for deeper meaning in her existence, she sets off a chain of events that may allow all of Equestria to break free from tyranny, and all ponies to choose their own destinies once more.
Based on the My Brave Pony: Starfleet Magic universe by Dakari King Mykan, credit to him for most of the OCs