User blog comment:JAlbor/Assassin's Creed: Black Flag Q&A Opportunity/@comment-71.62.19.14-20130816153457/@comment-13471981-20130816153948

You're a researcher working for Abstergo Entertainment, one of Abstergo's many branches. Not every employee at Abstergo Entertainment is a templar, in fact, most of them are just regular people, as you are as well. A developer has said it won't be a "press button to choose side: Assassin or Templar", so I presume you'll simply find out about the conflict through other means (Erudito maybe?).