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A recent interview confirmed that there will only be two factions present in the new 40K MMO. Perhaps there will be a third non-playable faction, but I don't think that's what most people were looking for.
"Strategy Informer: I assume you're going to divide up the playable races by factions? They only thing is, apart from ones like Imperial guard and Space Marines who can stick together, not all of the other races fit neatly into 'factions'. The Eldar, the Tau, the Necrons, Tyranids Chaos... had to generalise them. Are you going to try sticking with the traditional two factions or branch out to more?
Tim Campbell: We're going to have two overall factions in the game, and all of the playable races are going to fit into one or the other.
There are compelling reasons why that works in this situation and our game, and Games Workshops are completely on board with it so we're not doing anything that violates the IP or the fiction – the details though will be revealed in the near future."