Mary E. Pearson - Jenna Fox Chronicles 2-3

The Fox Inheritance: "Riveting, thought-provoking."—Suzanne Collins

Once there were three. Three friends who loved each other - Jenna, Locke, and Kara. And after a terrible accident destroyed their bodies, their three minds were kept alive, spinning in a digital netherworld. Even in that disembodied nightmare, they were still together. At least at first. When Jenna disappeared, Locke and Kara had to go on without her. Decades passed, and then centuries.

Two-hundred-and-sixty years later, they have been released at last. Given new, perfect bodies, Locke and Kara awaken to a world they know nothing about, where everyone they once knew and loved is long dead.
Everyone except Jenna Fox.

3-Fox Forever
Locke Jenkins has some catching up to do. After spending 260 years as a disembodied mind in a little black box, he has a perfect new body. But before he can move on with his unexpected new life, he’ll have to return the Favor he accepted from the shadowy resistance group known as the Network.

Locke must infiltrate the home of a government official by gaining the trust of his daughter, seventeen-year-old Raine, and he soon finds himself pulled deep into the world of the resistance—and into Raine’s life.