The Mane 6 hold a meeting discussing changes, and consider welcoming a new species... Until the five of the Mane 6 find out who the new species' leader is!
Come around and see the mixture of two stories. One were ponies start meeting changelings through the lenses of six ponies now, turned changelings, and another one of queens facing the changing of history through their eyes.
Pinkie Pie turns another page of notes, alone in the basement of Twilight's library. She hears a crash upstairs and then a sound like a flame being ignited. She hears him speak. "Chrysalis is going to be angry you're influencing the process."
Twilight and her friends knew each other from the start. Becoming heroes was unexpected, but welcome. Now that the wedding of Shining Armor draws near though, it's time to meet up with an old friend, and execute their true plan.
Twilight is awakened by Discord to find she- and all of Equestria- have been converted into changelings. With only a few pockets of resistance remaining, she must hurry to find her friends and bring them back to their senses defeat Chrysalis.