The Starship Enterprise and her crew must deal with a scientist haunted by his past, armed with a tool that could either revive his lost world in a new form or bring untold destruction. Meanwhile, the last two members of a dying race have made their way into the Enterprise's holodeck and have started up a simulated world to live in, populated by colorful talking ponies that seem to transcend the limitations of normal holodeck characters.

From another perspective, Twilight Sparkle and her friends must deal with strangers from another world who make claims that shake the very foundations of Equestrian history, science and philosophy. Can even the Magic of Friendship stand up to the possibility that the world is a simulation? Or do the ponies have what it take to prove to the strangers the truth of their existence?