As we all know, most Multiverses articles have been deleted and moved to Shoutwiki. This at first boggled my mind. What is the in-universe explanation for this?, I asked myself. Well, after a long night of watching the Doctor Who season 5 finale, it struck me like a Dalek extermination beam. Ladies and gentlemen, behold the continuity. :)
It all started in 4.000(.024) AM, when a Wazelian artist inadvertantly painted a picture of the TARDIS exploding. The painting went into private collections, and eventually came into the ownership of Nutay Rinkam, and old friend of the Doctor (he had helped her when the Daleks were posing as Zyrothan inventions during the Keel War). Using a timey-wimey phone, she called upon River Song.
Alarmed by her new knowledge, River left the words "Hello sweetie" on a cliffside on Inferno, prior to the rise of Hectocapitus. She then went to purchase a Vortex Manipulator from Seff Tintel, and went to ancient Petaurista and posed as... uh... Atrenid-Cleopatra.
The Doctor found the message, and immediately went to find her. His companion (Salsene-Amy) had recently lost her fiancee, Salsene-Rory. Upon finding River, and looking under Atrenid-Stonehenge, he found the Pandorica, a prison for the most feared being in the universe.
But then, the Pandorica sends out a signal throughout Obeidon, summoning all the members of an alliance against the Doctor. There are Daemons, Elisri, Raptors, Verplaatsen, Kerarans, Flesh Thieves, Typhons, Ravagers, Yraath, and even a Terrortooth for some reason. Salsene-Rory is revealed to be a plastic Salsene made by the Nightstalker, and then kills Salsene-Amy.
The rest is history. The Alliance imprisoned the Doctor in the Pandorica, allowing the TARDIS to explode. The explosion caused cracks in space-time, which soon swallowed the whole of Obeidon and resulted in the deletion of countless races. Plastic-Salsene-Rory watched Salsene-Amy for thousands of years until young Salsene-Amy could touch the Pandorica. The Doctor used the vortex manipulator to come to the modern day, where he managed to reboot the multiverse, creating multiverses.shoutwiki.com.
But he still didn't know what caused the TARDIS to explode! All he knew was that a ghostly voice had yelled "R'lyeh" moments before the explosion...
Aaaand there you have it. The unified theory of Wikia, Shoutwiki, and the Doctor Who Expansion. You're welcome.