The War of Emperium is a guild versus guild siege battle with the purpose of taking over Pron Fortress and reaping the rewards that come with it. Your fellow guild members are your battle allies, while members of other guilds are your enemies. All the guilds participating will have to compete with each other and attack Pron Fortress.
See more at http://www.playragnarok2.com/landing/RO2's WoE is different from RO1 but it is also fun.
BONUS: Check out this video by Gamespot on 10 things you should know about Ragnarok 2.
It is a great video for new players getting an overview of the game.