The Girl in the Box Series by Robert J. Crane

Sienna Nealon was a 17 year-old girl who had been held prisoner in her own house by her mother for twelve years. Then one day her mother vanished, and Sienna woke up to find two strange men in her home. On the run, unsure of who to turn to and discovering she possesses mysterious powers, Sienna finds herself pursued by a shadowy agency known as the Directorate and hunted by a vicious, bloodthirsty psychopath named Wolfe, each of which is determined to capture her for their own purposes...

Still haunted by her last encounter with Wolfe and searching for her mother, Sienna Nealon must put aside her personal struggles when a new threat emerges – Aleksandr Gavrikov, a metahuman so powerful, he could destroy entire cities – and he's focused on bringing the Directorate to its knees.