Injustice Book 2: Darkness in the Light (Naruto + Young Justice Crossover)

With his freedom regained, Naruto is left lost and unsure of what to do. The life of the anti-hero had torn down his relationships and the life of the mercenary had left him betrayed. Now, he finds himself on a team of young heroes, new burdens thrust upon his shoulders and new enemies coming out of the Light. Will he survive the coming storm? Book 2 in the Injustice Series.

This follows the events after Book 1: A Journeys Beginning and I highly recommend you go read that or else you'll have no clue as to what's happening in this story or how certain characters got to their current points in power and character development.