Fifteen years ago, Princess Twilight Sparkle, creator of the computer and fourth Princess of Equestria, vanished without a trace. She had been hard at work on something only she had any knowledge of, and when she disappeared, her knowledge and work did with her. Her son Arcturus took the loss hardest of anyone, and began a life as a delinquent, nothing more than a hacker and prankster.

But when a mysterious message appears on his mom's friend Trixie's phone, from a number that once belonged to his mom's old lab beneath her castle, Arc sets out on a journey to find his mom that will take him to the very place he thought was just a bedtime story: inside the computer itself.

Inside, he finds himself entangled in a plot to lure his mother into the open, so that these malignant programs may escape to the outside world and enslave all of Equestria. Only one pony he knows could possibly help him stop them -- the one pony he has been searching for his entire life.