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.
Throughout the month of November we learn more and more about the Niantic Project as well as an app called Ingress (released November 14/15). We learn that the Niantic Project appears to be a scientific project sponsored by the NIA to study the effects of something called the Shaper Mind Virus and something called Exotic Matter (XM).
Dr. Devra Bogdanovich, a quantum biologist and former professor in the Stanford Physics department, is asked to lead the project, which is overseen by Dr. Ezekiel Calvin, with unknown affiliations, and Ni Yuen, Director of the NIA. We also meet Dr. Oliver Lynton-Wolfe, a scientist with a very good sense of working with XM and making technology to use/interact with XM. Dr. Carrie Campbell, a linguist specialist who ends up looking into a language known as Shaper glyphs. Enoch Dalby, a musician.