The Shattered World
Vecna was slain — phylactery and all — by parties unknown. Kros, however, before it became the Shadow Wight and the Unmaker, found a small piece of Vecna’s body, and was able to use it to resurrect the undead god. Seeing an opportunity, Kros continued to ingratiate itself, helping Vecna to regain much of his former power in secret, before betraying and slaying him itself, gaining considerable power but somehow failing to achieve apotheosis. Nonetheless, Kros would later become the physical incarnation of pure elemental destruction after an accident involving a Sphere of Annihilation in Vecna’s tower — a result no doubt enabled by having absorbed Vecna’s essence.
Today the Lord of Secrets harbors an intense hatred of Arlen for muscling in on his domain of Secrets, but was left considerably weakened after somehow returning to undeath after being destroyed by Kros.
However, some speculate that the Vecna that returned after being destroyed by Kros is in fact an impostor, merely another power-hungry lich that saw an opportunity to advance its power. That the “new” Vecna displays numerous traits the “old” one did not — including possessing both hands and both eyes — lends enough credence to this theory that it cannot simply be dismissed.