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So this is a really really general, quick overview of the story. You must dig deeper in this wiki and other places to understand it all.
In July 2012, a comic artist named Tycho confronted people in a panel about a hidden truth. He was escorted away. On his web site, there were five posters posted. each contained a number of images, words and codes. They all seemed to indicate a conspiracy. There were also cards handed out that mentioned something called the Niantic Project and a phone number that first lead to a voicemail asking for information about Tycho, but later changed to an audio code that lead to geographic coordinates for the CERN lab in Geneva.
In November of 2012, a website, www.nianticproject.com went live. It was run by someone named P. A. Chapeau, a mysterious blogger who was investigating the Niantic Project. He began sharing videos, audios and leaked documents, all uncovering that the Niantic Project was more than a simple science project housed at the CERN lab.