Virgil is hurting. He can't take the blaming and angry words and hateful glares from the light sides. He doesn't believe Patton's kindness is genuine. The Prince's disapproval has finally breached his defenses, finally crumbled his walls, and now Virgil is done. Logan's completely logical reasoning why Virgil wasn't necessary was true, and he knew it too. Virgil was done with the light sides' cruelty, and when Thomas agrees that Virgil isn't wanted, Virgil breaks. The Darkness has found its prey, and it's time to go hunting.