Nibiru

Nibiru is a legend well-known in Babylonian history.

Legend of Nibiru
It tells the story of how a large object, either a planet known as Twelfth Planet, Planet X or Nibiru, will collide with Earth. It is referenced as "The Doomsday Event". In this event, god-like creatures called the Annuaki from the planet Nibiru will arrive on Earth.

Actual history
One known sentient of the planet was somehow captured inside a sarcophagus, it is unknown how and why it was imprisoned. This sentient was the most evil of the Anunnaki that for eons has been plotting its revenge and possessing animals in order to try and free itself. Its very first encounter was with the Spanish Conquestidors who were told of a crystal sarcophagus that was filled with black pearls, but when they found it the being inside possessed and controlled them drving them insane and forcing them to ransack almost every village that they were once friends with, eventually however they started to resist and hid the treasure underneath what is now Crystal Cove. A complex guide was created in order to make the treasure hard to find, first created by the Conquistadors who realised the power of the god inside. They then went their seperate ways, with the pieces of the disks scattered as well, but after many mysteries and mysterious (almost devine) interventions, were eventually found by Mystery Inc.. The Planispheric Disk was being deciphered giving Mystery Incorporated clues on certain keys from the ancient Mayan days. More ecently the word "Nibiru" has appeared in almost all of the incidents being uttered by the deceased or even decoded from the Planispheric Disk.

Season two
"Nibiru" spoke through the ghost of El Aguirre, leader of the Conquistadors as Mystery Incorporated left Mount Diabla. (Night on Haunted Mountain)

Abigail Gluck said it when Mystery Incorporated found her corpse. (The Midnight Zone)

Velma Dinkley searched on her website for any information on Nibiru and discovered it to be the doomsday event. Unknown by Mystery Incorporated, after they connected the Planispheric Disk together, the sarcophagus in the lost underground city uttered the word "Nibiru" and laughed. (Wrath of the Krampus)

Velma cobbled together a player for the Planispheric Disk, and it produced the word "Nibiru" also.

After solving a mystery, the real mummy Friar Serra returned to warn them of "Nibiru", a cataclysm that is inevitable unless "the dog dies". (Theater of Doom)

Nova was put in the hospital, placed in a deep coma. During one of his visits, the monitor turned off showing that she died. Suddenly she awoke and warned Scooby-Doo, "Nibiru, Nibiru is coming". (Dance of the Undead)

An Anunnaki possessed Nova and appeared in Scooby-Doo's nightmare telling him that Nibiru is coming. She told Scooby-Doo to destroy the cursed treasure before the evil Anunnaki was released within the sarcophagus. (Stand and Deliver)

When the gang attempted to destroy the Evil Entity, Nibiru arrived and all the planets were aligned. (Through the Curtain)