After you complete training on the Ingress mobile app, you will have to select a faction. There are two factions in the war, The Enlightenment and The Resistance.
Joining The Enlightened
The Enlightened are interested in the Portals and the mysterious energy that has begun to spread across the planet. They want to research the energy and find a way to utilize it to advance our society.
Joining The Resistance
The Resistance is scared of this new energy and they want to control it to prevent others from knocking down a domino that could be the end of our existence. They see fear in P.A.Chapeau's findings and want to shut it down as soon as possible.
The choice ultimately comes down to you and every agent plays a large part in the success of either campaign. One thing to note, is that once you pick a side, I think it is difficult to switch to the other team.